Bookkeeping for a US clinic on Jane: the honest guide

Jane is everywhere in US physical therapy, chiropractic, massage, mental health, and multidisciplinary clinics. What it is not is an accounting system, and it does not connect to one. There is no native QuickBooks or Xero integration and no scheduled export, so the only way your numbers get from Jane into your books is that a person pulls CSV reports and brings them across by hand every month.

The mechanics of that import are the same wherever you are, and they are covered in the Jane to QuickBooks and Jane to Xero guides. This piece is about the parts that are specifically a US problem: sales tax on what you sell, how you classify and pay your practitioners, and how HSA, FSA, and out-of-network money actually lands. If you want a quick read on where your own books stand first, the Clinic Close Scorecard takes about two minutes.

The Jane Payments trap, US edition

Jane Payments runs on Stripe and pays out on a rolling schedule about two business days after the charge, net of the processing fee. US rates run roughly 2.85% plus $0.25 for online or keyed cards and 2.6% plus $0.10 for in-person, though you should confirm your own plan. The result is the same problem clinics see everywhere: the deposit in your bank is a bundle of charges from a day or two ago, minus a fee you never see leave, so it never matches a single day's sales.

If you code that deposit straight to income, you double-count, because the revenue was already recorded at the invoice. The fix is a Jane Payments clearing account, exactly as described in how to reconcile Jane Payments. Book sales to revenue and into clearing, then clear each payout out to the bank and a merchant fee expense when it lands. Revenue is recorded once, the bank ties, and the fee is a deductible expense instead of vanishing.

Sales tax: your services are usually fine, your retail probably isn't

In most states, the treatment itself, the PT session, the adjustment, the massage, is a service that is not subject to sales tax. The trap is the retail side. Supplements, orthotics, braces, topical products, and equipment you sell over the counter are tangible goods, and in most states those are taxable. The moment a clinic sells products alongside care, it is a mixed business that has to separate taxable product sales from non-taxable services, charge tax on the right lines, and remit to the state.

Two things make this messier than it sounds. First, the rules and rates vary by state and sometimes by county and city, so there is no single answer. Second, economic nexus means selling into other states (say, shipping supplements to patients) can create a filing obligation somewhere you do not have a physical location. Practically, set up your chart of accounts so product revenue is separate from service revenue from day one, track tax collected in its own liability account, and get a state-specific read from a sales tax professional. Confirm treatment before you rely on any of this.

1099 vs W-2: the classification that drives your whole payroll

How you pay your practitioners is the biggest US-specific decision in a clinic's books, and it is not really a bookkeeping decision. It is a legal and tax classification, and getting it wrong is expensive.

If a practitioner is a W-2 employee, their pay runs through payroll with federal and state withholding, payroll taxes, and a W-2 at year end. If they are a 1099 independent contractor, you pay them as a vendor, withhold nothing, and issue a 1099-NEC if you pay them $600 or more in the year. The determination turns on control: who sets the schedule, who owns the client relationship, who provides tools and space, whether the practitioner works for others. Many clinics default everyone to 1099 because it is simpler, and some of those classifications would not survive scrutiny. This is worth a conversation with an employment or tax advisor, because reclassification back taxes and penalties are real.

For the books, the key point is that the practitioner's compensation, whether it is a percentage split, salary, or hourly, does not come out of your Jane Payments deposit. Jane only deducts the card fee. Comp is calculated separately, off Jane's Compensation Report or your own model, and paid through payroll or accounts payable. Tag it by practitioner so you can actually see profit by practitioner.

HSA, FSA, and out-of-network money

US clinics collect money in a few ways that need a little care in the books.

HSA and FSA cards are just cards as far as Jane Payments is concerned: they run through the same rails and settle in the same payouts, so they reconcile the same way. The nuance is on the patient's side, where eligible services and substantiation matter, not on yours. You do not need a separate revenue treatment, but a clean itemized receipt out of Jane helps your patients and keeps you out of their disputes.

Out-of-network and cash-based clinics, which are common in US PT and mental health, collect from the patient at the time of service and hand them a superbill to submit to their insurer for reimbursement. That reimbursement goes to the patient, not to you, so your revenue is simply what the patient paid. That is cleaner than in-network billing, but do not let the superbill confuse the books: you recognize the patient payment as revenue, and the insurer's reimbursement never touches your ledger.

In-network clinics that bill insurers directly have the harder version, where billed and collected are different numbers on different days and denials and adjustments hide in the gap. That is an accounts receivable problem: recognize revenue when earned, carry the receivable, and write down what the payer actually allows.

Prepaid packages and memberships

Package deals, class passes, and memberships are common in US clinics, and they are a liability, not revenue, until the visits are delivered. Booking a 10-pack as income on the day it sells overstates that month and distorts every margin. The full treatment, including gift cards, is in deferred revenue for clinics.

None of this is exotic. It is a clean chart of accounts that separates service and product revenue, a Jane Payments clearing account, comp posted by practitioner, sales tax tracked as its own liability, and revenue recognized when it is earned. Set it up once and the monthly close on a US clinic runs in an hour.