The dispensary is retail, and retail gets counted
A supplement order is not an expense on the day the box arrives. It is inventory, an asset on the shelf, and it becomes cost of goods sold only when a bottle actually sells. Clinics that expense purchases on arrival overstate costs in stocking months, flatter the months that follow, and can never say what the dispensary really earns. We carry stock as an asset, cycle-count it against the point of sale, and report margin by product line every month.
Three leaks get their own accounts. Expired stock is written off when it is pulled, dated and noted, so wastage becomes a visible number instead of a mystery buried in cost. Bottles opened for clinic use or handed out as samples move to a clinic-use account rather than vanishing from the count. And the product buttons in Jane or Practice Better have to map to the chart of accounts one for one, because a till that rings everything as one dispensary line produces a margin nobody can defend.
Some practices skip shelves entirely and dispense through Fullscript. The bookkeeping changes shape with them: no inventory, no counts, just a monthly margin remittance that belongs on its own income line, kept apart from clinical fees because it is a different kind of revenue with different tax character.
Four payment streams, four clocks
Deposits are not revenue; they are clues. Each stream lands on its own schedule, and each needs its own reconciliation before a month can close honestly.
| Stream | How it lands | What we reconcile |
|---|---|---|
| Visits paid at the desk | Terminal batch, net of card fees, next day | Day sheet to batch before the desk closes |
| Direct billing via Telus eClaims | One deposit, many patients, several insurers, days later | A receivable by insurer, cleared claim by claim |
| Fullscript payouts | Periodic margin remittance, no stock touched | Payout report to its own income line |
| Prepaid IV or visit packages | Cash today, care later | A patient-credit liability, released visit by visit |
Insurer paperwork adds one rule of its own. Extended-health plans reimburse the naturopathic visit, not the products, so every receipt must split service from supplement and show the practitioner's College of Naturopaths of Ontario registration number, or claims bounce and the front desk spends Friday reissuing paper. We set the invoice templates once so the split happens by default.
Exempt fees rewrite the cost side
Naturopathic services have been HST-exempt since 2014, which means no tax on consult invoices and no input tax credits on the 13% the clinic pays for rent, software and clinical supplies. We record service-side costs HST-inclusive, because that is what they genuinely cost, and budgets built any other way flatter themselves. IV therapy consumables, the bags, lines, sterile kits and the vitamins in them, sit on this clinical side too, tax included, because the drip is part of the exempt service rather than the shop.
Dispensary cost of goods stays on its own ledger for the opposite reason: those sales are taxable, they are the revenue that can eventually force HST registration, and once that happens input tax credits attach there and nowhere else. The books carry a running taxable-sales total so the threshold is watched rather than discovered, with the filing consequences handled inside Corporate Tax Filing.
One roof, delivered monthly
All of it runs inside End-to-End Accounting: bookkeeping, payroll for reception and clinic staff, financial reporting and tax filing under one roof. The stack is QuickBooks Online with Dext capturing supplier bills, tied to whichever platform runs your schedule and your till. Month-end arrives as a short pack: collections by stream, dispensary margin after write-offs, payroll, cash position and whatever moved enough to matter.
When the CRA writes, and a practice running exempt services beside taxable retail eventually gets a letter, CRA Audit & Review Support answers it from records we already keep. We run this monthly rhythm for naturopathic clinics across Mississauga and the GTA, with every engagement quoted in writing after a free 15-minute discovery call.
