Pharmacy Accounting in France: Obligations, Chart of Accounts and Balance Sheet

The accounting of a French pharmacy (officine) is commercial accounting under the BIC regime (industrial and commercial profits), even though the owner is a health professional. Its specific features: VAT at four rates (2.1%, 5.5%, 10% and 20%), a regulated margin on reimbursable medicines, supplier rebates capped by law, agreement-based income paid with a lag (dispensing fees, ROSP), and a stock that dominates the balance sheet.

Looking for a firm to keep the books of your pharmacy instead? Our specialist pharmacy accounting firm page sets out the engagement and the fees.

Updated 2 September 2026.

A French pharmacy (officine) is a business unlike any other, combining the constraints of a regulated health profession (professional duties, an agreement with the public health insurer, public service obligations) with those of a retail business exposed to market forces, margin pressure and the growing competition of buying groups. In 2026, owners also absorb new missions (vaccinations, pharmaceutical interviews, teleconsultation, rapid screening tests) and a structural reform of the pharmacy economic model that has been under way for several years.

This guide covers the accounting of the officine itself: the applicable tax regime, the owner's obligations, how the chart of accounts is organised, medicine VAT, stocktaking and reading the balance sheet. If you are instead looking for who should do that work, at what price and using what method, our dedicated pharmacy accountant page sets out the engagement, the fees and how a pharmacy file runs.

Key areas covered#

• Multi-rate VAT management (2.1%, 5.5%, 10%, 20%) and LGO software integration
• Legal structures: SEL (SELARL/SELAS), SPFPL (pharmacy holding company)
• Owner remuneration optimisation: salary vs dividends arbitrage
• CAVP retirement planning and supplementary savings (PER, Madelin contracts)
• ROSP: calculation, provisioning and optimisation
• Stock management and working capital (BFR)
• Pharmacy valuation and transfer (LBO, OBO, Dutreil)
• Payroll under the pharmacy collective agreement (IDCC 1996)
• Digital tools: LGO integration, monthly dashboards, e-invoicing compliance

Before going into detail, here are the six accounting features that set a pharmacy apart from an ordinary shop. Each is developed later in this guide.

1. BIC, not BNC. A pharmacy owner is taxed under the industrial and commercial profits regime (BIC), whereas most other health professionals declare non-commercial profits (BNC). The consequence is full commercial accrual accounting: stock, receivables, payables and invoices, with a BIC or corporation tax return depending on the structure.

2. VAT at four rates. Sales are split at 2.1%, 5.5%, 10% and 20% from the dispensing software (LGO) onwards. The monthly VAT return is checked by reconciling the turnover per rate in the software with the accounts.

3. A regulated margin. On reimbursable medicines the margin is set by ministerial order through the degressive smoothed margin (MDL): 10% up to 1.91 euros of manufacturer price excluding VAT, 7% from 1.92 to 22.90 euros, 5.5% from 22.91 to 150 euros, 5% from 150.01 to 1,930 euros and 0% above (order of 12 November 2018, in force since 1 January 2020).

4. Supplier rebates capped by law. Since 1 January 2026, rebates on generics are capped at 40% of the manufacturer price excluding VAT (20% for biosimilars) by the 2026 social security financing act. They are recorded as a reduction of purchase cost, never as income.

5. Agreement-based income paid with a lag. Dispensing fees and the ROSP public health bonus are paid by the health insurer after the fact; the ROSP is attached to the year in which the targets were met through accrued income.

6. A dominant stock. Twenty to forty days of turnover are tied up in stock: the physical count, valuation and impairment of expired and slow-moving items feed straight into the result.

These six features explain why a pharmacy's chart of accounts, monthly controls and balance sheet do not mirror those of any other retail business. The sections that follow take them one by one.

The turnover of a pharmacy is built around five main categories, each with its own margin and VAT regime. Reimbursable medicines (with a regulated retail margin) typically represent 55 to 65 percent of turnover and are taxed at 2.1 percent. Non-reimbursable medicines (over-the-counter advice products) account for 10 to 15 percent at the 10 percent VAT rate with a free margin. Parapharmacy and cosmetics make up 8 to 12 percent at 20 percent. Medical equipment such as orthopaedics and home-care devices represents 3 to 7 percent, at 20 percent or, for the appliances listed under article 278-0 bis of the tax code only, at 5.5 percent. Finally, dispensing fees account for 5 to 12 percent, taxed at 2.1 percent.

The dispensing fee, created by the pharmacy agreement with the health insurer, represents a growing share of pharmacy results. It is paid by the Assurance Maladie directly to the pharmacy and rewards the act of dispensing independently of the price of the medicine. In 2026 the fee per prescription (HDR) is 0.61 euros including VAT, the age-related fee (HDA, patients under 3 or over 70) 1.68 euros, the HDE fee 3.57 euros and the HC fee 0.31 euros, all subject to VAT at 2.1 percent (ameli.fr, page updated 17 April 2026). In the accounts these fees are tracked in an income account separate from sales of goods, so that the share of agreement-based income in turnover can be read directly.

Gross margin is the key indicator of a pharmacy. As a commonly observed order of magnitude, it sits between 28 and 34 percent of turnover including VAT, and varies sharply according to the generic substitution policy, the product mix (the ratio of reimbursable medicines to OTC and parapharmacy), negotiations with laboratories and wholesalers (year-end rebates), and location (urban, rural or shopping-centre pharmacy). A two-point difference in gross margin on a pharmacy with 2 million euros of turnover represents 40,000 euros of additional profit. That is the indicator to follow by product family, month by month, from the margin reports of the dispensing software reconciled with the accounts.

On the cost side, purchases of goods net of rebates weigh 68 to 72 percent of turnover, staff costs excluding the owner 12 to 16 percent, rent and rental charges 2 to 4 percent, depreciation 0.5 to 1.5 percent, financial charges 1 to 3 percent and other external charges 2 to 4 percent. The pre-tax operating result of a pharmacy sits, as a commonly observed order of magnitude, between 8 and 14 percent of turnover including VAT. Below 8 percent, the margin and cost structure deserves a line-by-line review; above 14 percent, the pharmacy sits at the top of the usual range.

VAT management is probably the most sector-specific tax complexity an officine faces. Unlike most retailers, who apply a single rate, a pharmacy juggles four distinct rates every day. Under the references in force in 2026, the 2.1 percent rate applies to reimbursable medicines and reimbursable magistral preparations (article 281 octies of the tax code), generics included where they are reimbursable, and to dispensing fees. The 10 percent rate covers magistral preparations, officinal products and medicines for human use that fall outside article 281 octies, that is non-reimbursable ones (article 278 quater). The 5.5 percent rate has a scope defined by article 278-0 bis, unrelated to the shelf a product sits on. On one side (paragraph A 2°, BOI-TVA-LIQ-30-10-50): appliances for disabled persons listed in chapters 1 and 3 to 7 of title II and in title IV of the list of reimbursable products and services (title III items on a list set by ministerial order), technical aids designed for disabled persons, diabetes self-monitoring supplies (lancing devices, glucose meters, insulin syringes and pens, test strips) and appliances for incontinence and stoma care. On the other side, over the counter, the products at the ordinary 5.5 percent rate: foodstuffs (A 1°), feminine hygiene products (A 1° bis) and condoms (A 1° ter). The shortcut of applying 5.5 percent to all medical devices or all home-care equipment is wrong: the rest of the medical equipment is at 20 percent, even when listed as reimbursable. The 20 percent rate covers parapharmacy, cosmetics and any product that qualifies for no reduced rate. Articles 281 octies and 278 quater are repealed on 1 January 2027 by ordinance 2025-1247 of 17 December 2025, which recodifies French VAT law: the references given here are those of 2026.

Several product categories regularly generate rate errors that can trigger a tax reassessment. Magistral preparations follow whether the preparation is reimbursable or not (2.1 or 10 percent). Homeopathic medicines, removed from reimbursement on 1 January 2021, fall under the 10 percent rate rather than 2.1 percent. Medical devices, connected or not, qualify for 5.5 percent only if they fall within one of the categories of article 278-0 bis (appliances for disabled persons in the chapters covered, technical aids, diabetes self-monitoring, incontinence and stoma care), not because of the shelf or the mere listing as a reimbursable product; otherwise the rate is 20 percent. For borderline products (parapharmacy, supplements, health products without marketing authorisation), the status of the product, not the shelf it sits on, decides the rate; in case of doubt the rate is checked in the official tax doctrine before configuration, not after an inspection. Configuring the dispensing software (LGO, such as Winpharma, LGPI, Opus or Pluspharmacie) by VAT rate is the starting point of the whole chain: it feeds the split of sales and then the monthly CA3 return, and a configuration error repeats itself on every till receipt.

A pharmacy is generally subject to standard-regime VAT, with a monthly CA3 return. The VAT collected at each rate is determined from the daily Z tickets of the dispensing software, the automated feed via the LGO to accounting software connection, and a monthly consistency check that reconciles sales turnover, returns and till discrepancies. Input VAT on purchases is fully recoverable: a pharmacy is not subject to a deduction proportion unless it carries on an exempt activity such as renting out space.

A pharmacy owner may practise in their own name. Unlike other health professionals, they then fall under the industrial and commercial profits (BIC) regime, not BNC: the official tax doctrine (BOI-BIC-CHAMP-60-30, paragraph 140) expressly places the profits pharmacists make from running their officine under BIC, because a pharmacy is a commercial business (fonds de commerce). The accounts are therefore full commercial accrual accounts, with stock, receivables and payables. This regime, historically the most common, has drawbacks: personal income tax on the entire profit even when not drawn, self-employed social contributions (URSSAF, CAVP) on the net BIC profit, no separation between the pharmacy and personal assets, and no arbitrage between remuneration and dividends. Representative case (illustrative): for a BIC profit of 150,000 euros and an owner in the 41 percent marginal bracket, CAVP and URSSAF contributions plus income tax can absorb in the region of half the profit, depending on family situation and the household's other income.

The Société d'Exercice Libéral (SELARL with limited liability or SELAS as a simplified joint-stock company) allows a move to corporation tax (IS) and is the structure most often studied from 80,000 to 100,000 euros of net profit, an order of magnitude to test against a simulation on the pharmacy's own figures. Social contributions are then based only on the remuneration actually paid; undistributed profit is taxed at IS (15 percent up to 42,500 euros, 25 percent above); dividends bear 18.6 percent of social levies (plus self-employed contributions above 10 percent of the capital in a SELARL); remuneration can be arbitraged between salary and dividends; and personal assets are separated. Representative case (illustrative, simplified assumptions): for a pharmacy profit of 200,000 euros, practice in own name (BIC) leaves net income of around 105,000 euros after roughly 95,000 euros of social charges and income tax. In a SELARL at IS with a salary of 80,000 euros, social charges fall to around 40,000 euros and IS on the 120,000 euros of residual profit is 15,000 euros at the reduced rate plus 5,000 euros at the standard rate, leaving net income (net salary plus retained cash) of around 140,000 euros. In this example the gap is around 35,000 euros a year. It depends entirely on the assumptions used (level of remuneration, distribution policy, family situation) and is not a general rule: the comparison is redone on the pharmacy's real figures.

The Société de Participations Financières de Profession Libérale (SPFPL) is the holding company specific to pharmacists. It holds the SEL shares and serves several purposes. First, the leveraged buy-out: the SPFPL borrows to acquire the SEL shares, and dividends flowing up from the SEL benefit from the parent-subsidiary regime (95 percent of dividends received are exempt, only a 5 percent share of costs and charges is taxable, an effective tax of 1.25 percent on the dividends), which repays the acquisition loan without passing through the pharmacist's personal income. Second, holdings in several SELs: the French public health code caps the number of holdings a pharmacy owner may have, directly or through an SPFPL, in other pharmacy SELs and makes such arrangements subject to formalities with the professional body; the exact cap and its conditions are checked against the text in force before any acquisition, after which the holding centralises inter-pharmacy financial flows. Third, the owner buy-out: the pharmacist sells SEL shares to their own SPFPL, recovering capital that is untaxed or lightly taxed on the capital gain, monetising part of the pharmacy's value without selling it. Fourth, bringing in a junior partner: the SPFPL allows an employed pharmacist to become a partner by acquiring holding shares without altering the operating SEL. The SPFPL is subject to specific ownership rules (only practising pharmacists may be majority partners) and to approval from the professional body; these arrangements are secured with a lawyer specialising in professional practice companies.

In a SELARL at IS, the pharmacy owner has four ways to draw income, to be arbitraged according to the situation. Manager or president remuneration is deductible from the company's taxable result and bears self-employed contributions (majority SELARL manager) or employee-equivalent contributions (SELAS president). Dividends are distributed after IS and then taxed at the flat tax (PFU) of 31.4 percent (12.8 percent income tax plus 18.6 percent social levies), or on election at the progressive scale; in a SELARL with a majority manager, dividends above 10 percent of capital plus current account bear self-employed contributions on top of the social levies, a frequent trap. A remunerated partner current account lets the pharmacist advance funds and receive interest that is deductible for the company within the BOFiP rate in force. Finally, in certain partial-transfer arrangements with a young partner, the seller may receive a fee for leasing the goodwill, with a specific tax regime to study.

As representative cases (illustrative), on a SELARL result before remuneration of 100,000 euros, around 60,000 euros gross of salary and 15,000 euros net of dividends gives a net tax and social burden of about 42 percent; at 200,000 euros, 90,000 euros gross and 40,000 euros net brings it to about 38 percent; at 300,000 euros, 100,000 euros gross and 80,000 euros net brings it to about 36 percent. These ranges are indicative and depend on family situation, marital regime, any property income and patrimonial objectives. In practice, for owners in a SELARL, self-employed status most often comes out cheaper in contributions for the same net income, provided social protection is supplemented with a Madelin contract (provident and supplementary pension cover).

The Caisse d'Assurance Vieillesse des Pharmaciens (CAVP) is the compulsory pension fund for all pharmacists registered with the professional body. It runs a basic scheme proportional to professional income (BIC profit or manager's remuneration), a supplementary scheme with a pay-as-you-go part and a funded part whose class is set by the reference income, and a flat-rate disability and death scheme. According to the official CAVP notice for 2026, the basic scheme charges 8.73 percent of income from 0 to 1 PASS (48,060 euros) for contributions due from 2025 onwards (the 2026 provisional call is still computed at 8.23 percent), plus 1.87 percent of income from 0 to 5 PASS (240,300 euros), from the first euro rather than above the PASS; the supplementary scheme costs 7,657 euros for the pay-as-you-go part plus 2,906 to 17,436 euros for the funded part depending on the class (3 to 13); the disability and death contribution is a flat 696 euros. A pharmacist may buy back retirement quarters for study years (up to twelve quarters), low-income early-career years and years worked abroad; the actuarial return on the buy-back (cost today against the expected pension supplement) is computed before deciding, because the operation is not always worthwhile.

Alongside the CAVP, a retirement savings plan (PER) builds a supplementary capitalised pension with immediate tax deductibility. For a pharmacist in a SELARL at IS, a company PER funded by the company is deductible from the taxable result, and voluntary payments are deductible from the pharmacist's taxable income within the Madelin ceiling or the available retirement-savings allowance. A pharmacist with 90,000 euros of taxable income who pays 15,000 euros into a PER saves 15,000 euros at the 41 percent marginal rate, that is 6,150 euros of tax, for a net savings effort of 8,850 euros on 15,000 euros invested; withdrawals from the PER will be taxed, which tempers the apparent advantage. Madelin contracts also let self-employed pharmacists deduct provident and health cover (deduction ceiling of 7 percent of the PASS plus 3.75 percent of taxable profit, capped at 3 percent of 8 PASS), supplementary pension cover (ceiling of 10 percent of taxable profit retained up to 8 PASS, plus 15 percent of the fraction of profit between 1 and 8 PASS, or 10 percent of the PASS if more favourable) and loss-of-employment cover (1.875 percent of taxable profit or 2.5 percent of the PASS). These ceilings come from article 154 bis of the tax code (version in force since 11 March 2023), with a 2026 PASS of 48,060 euros. The Madelin envelope is sized each year on the actual profit of the year: a few thousand euros of difference in the base means several hundred euros of tax either way.

The stock of medicines and parapharmacy is generally the largest item on a pharmacy's balance sheet, representing between 20 and 40 days of turnover depending on the supply policy. Two valuation methods are used: first-in first-out (FIFO), valued at the most recent purchase price and recommended for medicines with expiry dates, and weighted average cost, better suited to slower-moving stock. The annual inventory procedure (or quarterly where needed) runs in four steps: extracting the valued stock from the LGO, a counter-checked physical count with your team, treatment of discrepancies (unexplained shrinkage, expired goods, breakage), and recognition of provisions for impairment on expired or slow-moving products.

Working capital requirement is structurally high because you pay your suppliers (laboratories and wholesale distributors) before being reimbursed by the Assurance Maladie, on average 15 to 20 days later. Levers to optimise it include negotiating wholesaler payment terms, speeding up the SESAM-Vitale electronic transmission cycle for faster reimbursement, reducing dormant stock (products with no sale for more than 90 days), returning unsold goods to wholesalers, and taking supplier settlement discounts. The forecast cash position is tracked month by month, building in spending peaks (stock renewal before the festive season, fit-out investment) and seasonal troughs.

The balance sheet of a pharmacy is read through five items, which carry most of the information useful to the owner, the bank and a prospective buyer.

1. Stock (current assets). The first operating asset, it represents 20 to 40 days of turnover. Two questions arise: valuation (purchase price net of rebates, FIFO or weighted average cost) and impairment (expired goods, slow-moving lines). A stock that swells from one year to the next without a rise in turnover signals a supply or shrinkage problem, not wealth.

2. Goodwill (intangible assets). It appears only after an acquisition, at the price paid, and is not revalued afterwards: the book value of the goodwill therefore bears no relation to its market value. A pharmacy created by its owner shows no goodwill at all; one acquired long ago shows it at the original price.

3. The acquisition loan (financial debt). The heaviest liability of an acquired pharmacy, it is read together with the repayment schedule: outstanding principal, annual instalment, remaining term. The ratio of the annual instalment to the operating surplus (EBITDA) measures repayment capacity.

4. Equity. Capital, reserves and the result for the year, less the owner's drawings in own-name practice or dividends in a SEL. Equity that erodes while the result is positive means drawings exceed profit.

5. Health insurer receivables and supplier payables (working capital). Reimbursements due from the health insurer and complementary insurers sit in receivables; wholesaler and laboratory invoices in payables. The gap between the two, added to stock, gives the working capital requirement, which is structurally high in a pharmacy.

Restated EBITDA of a pharmacy: definition and adjustments#

EBITDA (excédent brut d'exploitation, EBE) is the pharmacy's result before depreciation, financial charges, exceptional items and tax. Restated EBITDA (or normalised EBITDA) corrects the accounting figure for items specific to the owner or non-recurring, to measure what the pharmacy really generates. The usual adjustments:

• Owner's remuneration: replaced by a market rate for an operating pharmacist, whether it is too high (SEL) or absent (own-name practice, where the profit includes the remuneration)
• Personal expenses recorded as operating costs (car, telephone, meals): added back
• Rent: brought to a market rent when the premises belong to the owner or their property company, whether the rent is under- or overstated
• Non-recurring items: indemnities, disputes, one-off subsidies, neutralised
• ROSP: attached to the year in which the targets were met, not the year of receipt

This restated EBITDA is the base for valuation multiples (see the transfer section) and for the banks' repayment capacity calculations.

A pharmacy is governed by the national collective agreement for retail pharmacy (IDCC 1996), which sets specific rules that structure the payslips. Jobs are classified by coefficient, from junior preparer to employed pharmacist, each coefficient pointing to a minimum salary under the agreement. The minimum amounts in euros are set by the salary amendment in force and revised regularly: they are read from the up-to-date text of the agreement (IDCC 1996, brochure 3052), not from a dated guide. Compulsory agreement-based premiums include a seniority premium under the agreement's scale, a qualification premium for diploma-holding preparers (BTS), and on-call allowances for night, Sunday and public-holiday duty.

Monthly payroll in a pharmacy covers payslips computed in line with the agreement grids, the monthly social declaration (DSN) with automatic transmission to the relevant bodies, sick leave and workplace accidents (subrogation, daily allowances), paid leave, employer and employee contributions with the general reduction on low salaries, and the compulsory company health cover with the minimum 50 percent employer contribution.

Transferring a pharmacy can take several forms with radically different tax consequences. A sale of the goodwill means the pharmacy is sold as a business; the seller realises a gain subject to professional capital gains tax, while the buyer bears transfer duties. A sale of SEL shares, where the pharmacy is run through a SELARL, carries registration duties for the buyer under the scale for transfers of company shares (article 726 of the tax code), distinct from the scale for transfers of a business (article 719); the seller's gain is taxed at the flat tax of 31.4 percent (12.8 percent income tax plus 18.6 percent social levies) or, on election, at the progressive income tax scale. The contribution-and-sale mechanism under article 150-0 B ter of the tax code allows shares to be contributed to a holding controlled by the seller; for disposals made from 21 February 2026 (law 2026-103 of 19 February 2026), the tax deferral is kept only if at least 70 percent of the sale proceeds are reinvested in an eligible economic activity within three years, with the reinvested assets held for five years (previously 60 percent within two years), letting capital be redeployed before the gain is taxed. Finally, gifting before sale through a Dutreil pact (article 787 B) can apply to the shares of the SEL running the pharmacy, granting a 75 percent exemption on the transferred value for gift or inheritance duty, subject to a two-year collective holding commitment followed by a six-year individual commitment for transfers made from 21 February 2026 (law 2026-103, article 8) and a management function held for three years after the transfer; luxury assets are excluded from the exemption.

A pharmacy is valued by combining several methods, the multiples commonly quoted being orders of magnitude with no normative value: a multiple of turnover including VAT (70 to 100 percent), a multiple of restated EBITDA (5 to 7 times), corrected net assets (revalued book value), and the comparables method (price per square metre by area). Specific valuation points to check include the quality and stability of turnover over three years, dependence on local prescribers, the remaining term of the commercial lease and renewal conditions, the quality of the fixed assets (fit-out, LGO, robotic equipment), and the generic substitution rate and ROSP level. A dispensing robot or automated system pushes the value up, depending on its condition and age, while a precarious lease or ageing prescribers justify a discount; there is no scale, and these adjustments are negotiated on the evidence.

On the accounting side, a transfer runs in stages. Twelve to twenty-four months before, the accounting result is restated to reveal the true EBITDA, adding back excess remuneration, personal expenses recorded in the accounts and exceptional charges. During buyer due diligence, the financial statements are checked over three years, along with the VAT split, the stock and any potential employment disputes. The transfer is then structured, choosing between a sale of the business or of shares, optimising the gain and structuring the buyer's SPFPL. Bank financing is arranged with a seven-to-ten-year business plan presenting the normalised EBITDA, the repayment capacity and the initial working capital requirement. After the transfer, the seller is supported on declaring the gain, the available tax options and reinvestment.

The accounts also have to be secured against the reassessment risks pharmacies face: incorrect VAT splits (applying 20 percent to products that should be at 2.1 or 5.5 percent, which can lead to a VAT recovery over the last three years plus a 40 percent penalty for deliberate breach if systematic), reclassification of supplier rebates, poorly allocated mixed charges, under-declared ROSP, and URSSAF inspection of social contributions. The defence is a documented review file, built from monthly review of collected and deductible VAT, quarterly reconciliation of software, accounting and declared turnover, consistency checks on supplier rebates, and a year-end review of deductible charges.

The Rémunération sur Objectifs de Santé Publique (ROSP) is an annual payment from the Assurance Maladie, calculated on quality-of-dispensing indicators. Its amount varies widely from one pharmacy to another; it is read on the annual statement from the health insurer and reconciled with the accrued income recorded, so it is a recurring source of income to be steered rather than a marginal extra. The main indicators are the generic substitution rate (ROSG), prescribing within the generic register, the number of pharmaceutical interviews (for vitamin K antagonists, asthma and direct oral anticoagulants), support for hospital discharges and shared medication reviews. Their thresholds and weightings are set by the pharmacy agreement and revised by amendment: they are read on the pharmacy's Ameli Pro dashboard, not in a guide.

The accounting treatment of the ROSP is where pharmacies most often slip. Because the payment arrives with a lag, usually in the first half of the following year, the income belongs to the year in which the targets were met, not the year it lands in the bank. The estimated ROSP is therefore recorded at each year-end as accrued income, so that the result reflects the performance actually delivered over the period. Skipping this step understates one year and overstates the next, distorting both the profit and loss account and any valuation built on it.

Steering the ROSP is as much an operational task as an accounting one. It means reviewing the monthly ROSP dashboard available on Ameli Pro to anticipate where the pharmacy stands against each target, configuring alerts in the dispensing software to flag substitutable prescriptions that were not substituted, and folding the expected ROSP into the tax and social result for the year. A two-point gap on the substitution rate, caught in June rather than discovered the following spring, is often enough time to recover the bonus. Treating the ROSP as a live indicator, not a year-end surprise, is what keeps the accounts and the operations in step.

In 2026 the connection between the dispensing software (LGO) and the accounting software automates the import of daily sales split by VAT rate, the reconciliation of Assurance Maladie reimbursements through the SESAM-Vitale feed, real-time tracking of stock and supplier purchases, and automated bank reconciliation of wholesaler and Assurance Maladie flows. The benefit is twofold: the multi-rate VAT split stops being a manual, error-prone task, and the owner gains figures that are current rather than three months old.

The LGO landscape in 2026 is concentrated around a handful of systems: Winpharma (Pharmagest), LGPI (Alliadis), Opus (Cegedim), Pluspharmacie (PHR), Pharmactiv and a few others. The mode of exchange with the accounts (periodic file export or automated connection) depends on the vendor and the installed version, and is checked with the vendor before the bookkeeping chain is organised. Knowing which connection your LGO supports matters in practice, because it determines whether the monthly close can be largely automated or whether it relies on manual re-keying that reintroduces VAT-split errors.

From this data a monthly management report is produced. On the financial side it covers turnover including VAT and its year-on-year change, gross margin by product family, forecast versus actual operating surplus, net cash and a three-month cash projection, and working capital with stock rotation. On the quality and compliance side it tracks the generic substitution rate against the ROSP target, the number of pharmaceutical interviews carried out, unexplained shrinkage as a percentage of stock, and the value of expired goods. On the social side it follows the payroll bill against budget, overtime and premiums under the pharmacy collective agreement, and absenteeism and replacement cost. A dashboard of this kind turns the annual accounts into a tool the owner can act on month by month, well before the year is closed.

The electronic invoicing reform (article 91 of the 2024 finance act) applies to a pharmacy as to any VAT-registered business, in two parts. Receiving electronic invoices has been compulsory for all businesses since 1 September 2026, which requires having chosen an accredited platform (PDP). Issuing them has applied since 1 September 2026 to large and mid-sized companies and applies from 1 September 2027 to SMEs, very small businesses and micro-enterprises, that is to almost every pharmacy; it covers invoices between VAT-registered parties (institutions, health professionals, inter-pharmacy invoices for locum arrangements or loans of medicines). Sales to private individuals at the counter do not give rise to an electronic invoice, but they fall under e-reporting: the periodic transmission to the tax authorities of transaction and payment data, at a frequency set by the pharmacy's VAT regime (every ten days under the monthly standard regime), with a penalty of 250 euros per missing transmission capped at 15,000 euros a year.

The practical question for an owner is which accredited platform to choose and how to bring the information system into line. The choice is made according to the LGO and the accounting software already in place, so that the e-invoicing and e-reporting flow connects cleanly to the existing setup rather than becoming a parallel channel reconciled by hand. The official list of accredited platforms is kept by the tax administration on impots.gouv.fr.

Pharmacies are among the sectors the tax authorities monitor most closely, precisely because their multi-rate VAT is complex. The most common error is an incorrect VAT split, such as applying 20 percent to products that should be taxed at 2.1 or 5.5 percent, or the reverse. Where the error is systematic, the authorities can demand a VAT recovery over the last three financial years plus a 40 percent penalty for deliberate breach, which turns a configuration oversight into a significant liability. A second recurring issue is the reclassification of supplier rebates: year-end rebates from laboratories must be correctly recorded as a reduction of purchase cost, and a poor treatment can artificially inflate the deductible charges. Since 1 January 2026, the social security financing act for 2026 caps rebates on generics at 40 percent of the manufacturer price excluding VAT (20 percent for biosimilars): the framework contract, the credit notes received and the rebate accounts must stay consistent with those caps. A third is poorly allocated mixed charges, where personal expenses of the owner (car, telephone, meals) are recorded as pharmacy operating costs and can be added back on inspection.

Two further risks are easy to underestimate. The ROSP paid by the Assurance Maladie is taxable income, so omitting it or recording it late can constitute an irregularity, which is another reason the year-end provision matters. And URSSAF inspections, which are frequent in this sector, check that employees are correctly affiliated, that employer contributions are properly calculated, and that the general reduction in contributions is applied correctly.

Protection against all of this is structural rather than reactive. It rests on a monthly review of the collected and deductible VAT accounts, a quarterly reconciliation of the dispensing-software turnover against the accounting turnover and the turnover declared for VAT, a consistency check on supplier rebates compared with the framework contracts, a year-end review of deductible charges to isolate mixed costs, and a documented review file. That file is the first line of defence in the event of an inspection, because it shows that the figures were checked as the year ran rather than assembled after the fact.

Two questions come up repeatedly, and both are decisions an owner should take with figures in front of them rather than on instinct. The first is when to move to a SELARL. The switch is most often studied when the BIC profit exceeds 80,000 to 100,000 euros; below that level, the cost of setting up and running the company may not justify the tax gain. The right approach is a comparative three-year simulation, so the decision rests on projected reality rather than on a rule of thumb. The second is whether to hold the commercial premises through a separate property company. If you own the premises where you run the pharmacy, separating the property holding (through an SCI or directly) from the operation (the SELARL) is generally advisable: it makes transfer easier, lets the pharmacy pay a deductible rent, and protects the property assets if the business runs into difficulty.

Bringing in a partner is a third frequent situation. When an employed pharmacist wants to become an associate, several routes exist: a direct sale of SELARL shares, entry into the capital of an SPFPL, or the creation of a new SEL under joint ownership. Each has different tax and legal consequences, and the accountant coordinates the operation with a lawyer specialising in libéral company law so that the chosen route fits both the seller's and the junior partner's objectives. The same applies to holdings in several pharmacies: a pharmacist may own or co-own only one officine, but may hold shares, directly or through an SPFPL, in SELs running other pharmacies, within a cap set by the public health code and subject to formalities with the professional body; the exact cap is checked against the text in force, with a specialist lawyer, before any arrangement.

On retirement, the pharmacist contributes compulsorily to the CAVP for both the basic and supplementary pension, with a legal retirement age of 64 following the 2023 reform; the CAVP pension depends on the number of points acquired and the value of the point at departure, which is why supplementing it with an individual or collective PER is strongly recommended. Across all of these decisions, the common thread is that the consequences are modelled on the pharmacy's own figures before the choice is made, never on profession-wide averages: every representative case in this guide is redone with real data. This guide informs; a decision specific to your situation needs a review of your figures, your documents and the law in force.

For the reader who would rather entrust this work than master it, here is what the accounting engagements of a pharmacy cover in practice, from recurring bookkeeping to one-off work:

• Bookkeeping: sales split by VAT rate retrieved from the LGO, bank reconciliations of wholesaler and health insurer flows, monthly VAT returns
• Year-end: stock count and impairment, accrued income for the ROSP, annual accounts and tax return, with a balance sheet read item by item as in the section above
• Structure and remuneration: own name, SELARL and SELAS compared on real figures, arbitrage between manager's remuneration and dividends, Madelin envelope and CAVP
• Payroll: payslips under the pharmacy collective agreement (IDCC 1996), monthly DSN, absence tracking
• Transfer: restated EBITDA, sale or acquisition file, choice between selling the business or the shares

The scope, working method and fees of a pharmacy engagement are set out on our pharmacy accountant page.