A physiotherapy clinic's card statement rarely matches its schedule of fees, and the mismatch is the whole story. Much of a clinic's revenue never touches the terminal at all: insurers pay their share through direct billing, workplace and motor-vehicle claims follow their own channels, and what the patient actually hands over at the desk is often only the uncovered balance. That balance is small — and small payments are exactly where per-transaction fees do their quiet damage, and where the difference between an in-person rate and an online rate stops being a rounding error.
This guide prices the part of clinic revenue that does run on cards: patient balances, booking prepayments, package and gift-card sales, and cancellation or no-show charges. Rates were checked on 2026-10-15 from the sources named in the table. The worked example is an illustration from those published rates, not a quote, and it deliberately uses patient-paid volume rather than total clinic revenue — the most common mistake in comparing processors for a health clinic is pricing the wrong denominator.
Why a physiotherapy clinic's card volume is smaller — and pricier per dollar — than it looks
Direct billing rearranges the money before a card is ever presented. As one Ontario clinic explains it to patients, when a plan covers 80% of a visit the patient pays the other 20%; the clinic bills the primary insurer first, coordinates what it can, and issues a receipt for anything the patient pays directly and claims back. Workplace-injury and motor-vehicle cases are billed through their own programs. The practical result for processing is that a busy, healthy clinic can have modest card volume with a low average ticket — a combination that punishes percentage-plus pricing with a large fixed component, and rewards paying attention to the cents column that most rate advertising treats as an afterthought.
The second stream is payment for commitment rather than treatment: online booking prepayments, cards stored on a patient profile, and e-invoices for outstanding balances. Clinic software builds these in — Jane, the practice platform many Canadian clinics run on, describes stored cards, online booking prepayments, and e-invoicing as core payment features, and links them to enforceable cancellation policies and fewer no-shows. Every one of those transactions is card-not-present, so the clinic pays online rates for the administrative payments that keep its schedule full, even though the treatment itself is delivered in person.
The third stream is the smallest and the most sensitive: the late-cancellation or no-show charge. One Ontario clinic's published policy charges the full treatment fee for a cancellation inside 24 hours or a missed appointment, and notes that those charges cannot be billed to the patient's insurance provider. So the charge lands entirely on the patient's card, at whatever rate the clinic's setup applies, in a transaction nobody wanted to have. Getting its cost and its handling right matters more for trust than the cents involved — but the cents still add up across a month of missed appointments.
The rates on the table, checked 2026-10-15
| Option | In-person | Online / prepay / invoice | Interac debit in person | Monthly fee |
|---|---|---|---|---|
| Jane App Payments (integrated software) | 2.6% + 10¢ | 2.85% + 25¢ | — | Software subscription is separate |
| Helcim (interchange-plus; published averages) | 1.79% + 8¢ average | 2.31% + 25¢ average | Priced on interchange-plus | None |
| Square (flat rate) | 2.5% per credit transaction | 2.8% + 30¢ card-not-present · 3.3% + 15¢ keyed | 0.75% + 7¢ | None |
| Moneris Flat Rate | From 2.65% + 10¢ | Quote / plan-dependent | $0.12 flat per transaction | Plan and hardware dependent |
About the Jane figures: an independent review of Jane for allied-health practices lists Jane Payments at 2.6% plus 10¢ in person and 2.85% plus 25¢ online, identifies Stripe as Jane's payment partner, and reports confirming with Jane that the processing fee is not marked up. Helcim's own comparison table publishes the same Jane rates alongside its averages. That cross-checking is why those figures are in the table — and the same standard should apply to any rate a salesperson quotes verbally: if it is not published somewhere you can re-check, it is not yet a price, it is a promise.
Helcim's averages need the usual interchange-plus caution. Its published markup at the lowest volume tier is interchange plus 0.40% and 8¢ in person and interchange plus 0.50% and 25¢ online, so the average a clinic actually sees depends on its patients' card mix. The federal small-business agreement — Visa and Mastercard cutting eligible domestic consumer credit interchange by up to 27%, to a weighted in-store average of 0.95%, with the government expecting processors to pass savings through — reaches an interchange-plus clinic automatically and a flat-rate clinic only when the provider lowers its rate.
Worked math: $18,000 a month in patient-paid card volume
The illustration: $18,000 a month actually collected by card from patients — 200 payments averaging $90. In the mixed case, half is paid in person at the desk and half arrives online through booking prepayments, stored cards, and e-invoices (100 payments each way). Processing only; software subscriptions and taxes excluded.
Jane Payments, all in person: $18,000 × 2.6% = $468.00, plus 200 × 10¢ = $20.00. Month: $488.00. Mixed half online: in person $234.00 + $10.00 = $244.00; online $9,000 × 2.85% = $256.50, plus 100 × 25¢ = $25.00, for $281.50. Mixed month: $525.50.
Square flat rate, mixed: in person $9,000 × 2.5% = $225.00. Online $9,000 × 2.8% = $252.00, plus 100 × 30¢ = $30.00, for $282.00. Mixed month: $507.00.
Helcim at published averages, all in person on a standalone terminal: $18,000 × 1.79% = $322.20, plus 200 × 8¢ = $16.00. Month: $338.20 — with the important condition that a standalone terminal does not run the clinic's booking prepayments or stored-card no-show charges inside its practice software.
The reading: the channel mix alone moves the integrated bill by about $37 a month on this volume — the same clinic, the same patients, a different door for the money. The standalone average is about $169 to $187 a month below the flat-rate and integrated mixed figures, which is the size of the cheque a clinic writes for integration and online collection combined.
None of that makes the standalone terminal the automatic winner. A physiotherapy clinic's scarcest resource is front-desk attention at changeover time, and a payment that reconciles itself against the appointment record is worth something real. The point of the arithmetic is narrower: the premium is measurable, it grows with the share of payments that move online, and a clinic that drifts from mostly-desk to mostly-prepay without re-pricing its processing is making an expensive decision by accident.
Cards on file, prepayment, and the no-show charge
Prepayment and stored cards solve a scheduling problem first and a payments problem second: they make a cancellation policy enforceable without an awkward phone call, which is precisely how clinic software presents them. Price them as what they are — online transactions. A no-show charge run on a stored card pays the online rate and its larger fixed fee; on a $90 charge at Jane's online rate that is $2.82 in processing on a payment the clinic would rather never take. Clinics cannot move that particular cost to the insurer — the published policy cited above is explicit that cancellation charges cannot be billed to insurance — so the charge, and its fee, sit between the clinic and the patient alone.
Two habits keep this stream clean. Keep the stored-card consent and the cancellation policy in the same conversation at intake, so a charge is never a surprise; a disputed no-show charge costs more in staff time and goodwill than any fee in the table. And review the prepay mix quarterly: if online prepayment is now the majority of collections, the comparison that mattered when the clinic signed up — the in-person rate — is no longer the rate that decides the bill.
Interac debit for small balances
Patient balances are the natural home of Interac debit, and the published figures show why the tender matters at small tickets. On Moneris's flat rate, Interac debit is $0.12 per transaction regardless of amount; a $45 balance paid by credit at 2.65% plus 10¢ costs about $1.29. Square prices in-person debit at 0.75% plus 7¢ — about $0.41 on that same balance — cheaper than credit, more than a flat debit fee. On a run of small balances, orthotics deposits aside, debit-first presentation at the desk is worth more than a tenth of a percent negotiated off a credit rate the balance was never going to be paid at. As always, the patient's choice governs: steering means making debit easy and visible, never blocking a card a patient needs to use.
Decision framework: stay integrated or add a standalone terminal
- Measure patient-paid volume, not revenue. Pull one month and total only what patients paid by card. If direct billing carries most revenue, your processing decision is a small-ticket decision.
- Split that volume by channel — desk, prepay/online, stored-card charges. Price each channel at its own rate before comparing any two processors.
- Put a dollar figure on integration using the worked-math method. Pay it knowingly for reconciliation and booking features, or stop paying it — either is defensible; drifting is not.
- Make debit the easy default for balances, and confirm your processor's actual Interac price, flat or percentage-based, in writing.
- Re-run the comparison when the mix changes — a new online-booking push, a second location, or a package program can move the answer more than any negotiation.
A note on steps: this is a pricing and decision guide, not a clinical or how-to procedure, so the framework above is the actionable part rather than a numbered fix.
Disclaimer: general information about payment processing costs only — not financial, accounting, tax, or health-care business advice, and not advice about insurance billing rules, which vary by insurer and province. Rates were checked on 2026-10-15 from the sources named in the table and can change; confirm current pricing before signing.
FAQ
Does direct billing reduce what a clinic pays in card fees?
It reduces the volume that runs on cards — the insurer's share never touches the terminal — but it leaves a smaller average patient payment, which makes the per-transaction part of the fee proportionally larger. Price processors on patient-paid volume and ticket size, not on clinic revenue.
What does Jane Payments charge?
Published figures checked for this guide list 2.6% + 10¢ in person and 2.85% + 25¢ online. An independent allied-health review identifies Stripe as Jane's payment partner and reports that Jane confirmed it does not mark the fee up; Jane's software subscription is a separate cost from processing.
Why do no-show charges cost more to process than desk payments?
A charge on a stored card is card-not-present, so it prices at the online rate — for example 2.85% + 25¢ instead of 2.6% + 10¢ on Jane Payments. Clinics also cannot bill cancellation charges to the patient's insurer, per published clinic policies, so the full charge and its fee stay with the patient and the clinic.
Is a standalone terminal worth it for a small clinic?
On the worked example, a standalone terminal at published interchange-plus averages cost about $338 a month against roughly $507 to $526 for mixed-channel flat and integrated options on $18,000 of patient-paid volume — but it does not run booking prepayments or stored-card charges inside the practice software. The saving is real; so is the manual work it returns to the front desk.