The deposit Jane Payments sends to your bank is not your revenue. It is a batch of patient payments with the processing fees already taken out, arriving about two business days after the visits. If your bookkeeping treats those deposits as income, your revenue is understated, your fee expense disappears, and any HST you collect through Jane can end up reported on the wrong numbers.
Jane is very good at running a clinic day. Where practice owners get tripped up is the gap between what Jane says patients paid and what shows up in the bank. Those are two different numbers on two different dates, and clean books have to hold both.
What actually lands in your bank
Jane Payments batches your card transactions and pays them out on a rolling schedule, typically about two business days behind the appointment. Each deposit is the net figure: the total your patients paid, minus the processing fee on every transaction. In Canada that fee is currently 2.5 percent for in-person credit cards and 2.75 percent online, so $1,000 of online payments arrives in your account as $972.50.
Refunds muddy it further. When you refund a patient, Jane nets it against that day’s payout, so a deposit can shrink for a reason that has nothing to do with a slow week. And the two-day lag means the last few days of every month land in the next one, which quietly shifts revenue across month end and, worse, across year end.
Why “deposit equals revenue” wrecks the books
Booking each deposit as income feels tidy, but it understates what the practice actually earned, because the fees were stripped out before the money arrived. CRA expects gross income on your return, with the processing fees shown as an expense. Report the net and your revenue line is wrong, your expense line is missing, and anyone reading the statements, from a lender to a potential buyer, sees a smaller practice than the one you run.
It also hides what card acceptance really costs you. Most clinic owners have never seen their annual processing fees as a single number. It is usually thousands of dollars, and it is deductible, but only if the books capture it instead of letting it vanish inside the deposits.
The HST side of your Jane numbers
If everything you bill is exempt care, physiotherapy or chiropractic treatment for example, HST barely touches your Jane setup. The moment your clinic has both exempt and taxable income, massage therapy, product sales, or insurer reports, the deposit problem gets sharper. HST is owed on the full price the patient paid, not on the net amount that reached your bank. A clinic that files from bank deposits is remitting from understated numbers, and that is the kind of gap CRA finds quickly in a review.
Processing fees
Card processing is a financial service, so Jane Payments transaction fees carry no HST. There is nothing to claim back on the per-transaction cost.
Your Jane subscription
The monthly Jane software fee is a taxable supply, so it does include tax. Registered clinics may recover the portion tied to their taxable activities.
What reconciling actually means here
Reconciliation is the monthly habit of proving that Jane’s reports and your bank statement tell the same story. Jane’s payout reports show which patient payments make up each deposit and what was deducted in fees. Good books record the gross revenue from those reports, post the fees as their own expense line, and match every deposit to its batch, including the payments still in transit at month end.
When that habit slips, the symptoms are familiar. Revenue in Jane never quite agrees with revenue in the accounting file, a missing payout goes unnoticed for months, and year-end becomes an archaeology project. For a taxable practice like a massage therapy clinic, the stakes are higher again, because the HST return depends on the same gross numbers.
Common questions
Can I just report the net deposits and keep it simple?
No. Income is reported gross, with fees as an expense. On small numbers the difference looks harmless, but across a year it misstates both lines, and if any of your income is taxable for HST, a net-based filing is wrong from the start.
Do Jane Payments fees have HST I can claim back?
Generally no. Payment processing is treated as an exempt financial service in Canada, so there is no tax buried in the per-transaction fee to recover. The software subscription is different, and so are some bundled extras, which is why those lines are worth splitting properly in your books.
What about cash, e-transfers, and direct insurer payments?
They still belong in your revenue, but they arrive on their own timelines and never appear in a Jane Payments payout. A complete reconciliation picks them up too, which is one more reason deposits alone cannot be your source of truth.
If your Jane numbers and your bank account have stopped agreeing, that is a bookkeeping problem with a known fix. Tell us about your clinic and we will get the books telling the truth again.