Jane App Accounting & Bookkeeping for Clinics

Jane App Is Practice-Management Software, Not Accounting Software

Jane App runs the front of your clinic: online booking, scheduling, charting, billing, insurance claims, and — through Jane Payments — card processing. It is the system many health and wellness clinics across Canada live in day to day, and it produces a lot of useful financial data.

What it is not is accounting software. Jane does not maintain a general ledger, track your operating expenses, run formal payroll remittances, or prepare your HST and tax filings. Treating Jane as your “books” is the single most common mistake clinic owners make. Jane is the source of your revenue data; your accounting file (QuickBooks Online, Xero, or similar) is where that data is reconciled, combined with expenses, and turned into financial statements and tax returns.

How Jane Connects to Your Accounting (Exports, Not a Sync)

Jane does not directly connect to any accounting platform with an automatic, real-time sync. Instead, its financial reports export to Excel/CSV, formatted so they can be imported into QuickBooks Online or Xero, and Jane publishes import guides for doing so.

In practice, most clinics don’t import every individual transaction. The more reliable approach for a typical clinic is a monthly summary reconciliation: take Jane’s billing and payments totals for the period and reconcile them to your bank, recording revenue, processing fees, and receivables in your accounting file. This keeps the books clean without drowning in line-by-line imports.

The Monthly Reconciliation: Jane Reports → Bank

The heart of Jane App bookkeeping is reconciling what Jane says you billed and collected against what actually landed in your bank account. Four things routinely cause discrepancies:

• Timing. A service billed in one month may be paid in the next, and insurer payments lag further still.
• Net deposits. Jane Payments deposits arrive after processing fees are deducted.
• Insurance receivables. Direct-billed claims create amounts owed to you that haven’t been paid yet.
• Unapplied credits. Prepayments and account credits sit on patient accounts until used.

A disciplined monthly close catches these while they’re small. Quarterly or annual catch-ups let them compound into errors that are expensive to untangle.

Jane Payments and Processing Fees

If you process cards through Jane Payments, the amount deposited to your bank is the gross transaction value minus processing fees. On Jane’s reports the fee shows as a negative line item, and the Jane Payments Transactions Report totals the fees for the period.

For accurate books, record the gross revenue and book the processing fees as a separate expense — don’t simply record the net deposit as your income, or you’ll understate revenue and lose a legitimate deductible cost. Over a year, processing fees on a busy clinic add up to a meaningful expense line.

GST/HST Coding in Jane: Exempt Services vs. Taxable Products

Jane lets you flag each item as taxable or non-taxable, and getting those settings right is what makes your sales-tax tracking trustworthy. Across Canada, many regulated professional services are GST/HST-exempt — with one important exception: registered massage therapy is taxable, not exempt, because it isn’t on the federal exemption list. Retail products (supplements, orthotics, oils, equipment) are taxable regardless of your service status. The rate you charge on taxable items depends on your province — for example, 13% HST in Ontario versus 5% GST in Alberta.

Set your Jane item tax settings to match your profession’s status and your province’s rate, and keep taxable product revenue clearly separated from exempt service revenue. That separation drives whether you have to register for GST/HST and how much you remit. If you’re in Ontario, confirm your profession’s treatment on its practice page — for example chiropractic, physiotherapy, massage therapy, or naturopathy — and see do wellness clinics charge HST on products? and the HST registration threshold.

Packages, Memberships, Gift Cards: Deferred Revenue

When a patient prepays for a block of visits, buys a membership, or purchases a gift card, you’ve received cash but haven’t yet earned the income. Recording it all as revenue on the purchase date overstates that month and distorts your margins.

The correct treatment is deferred revenue: record the prepayment as a liability and recognize income as each session is delivered or the gift card is redeemed. Jane’s reports distinguish billed, paid, and unapplied amounts, which gives your bookkeeper what they need to make this adjustment cleanly.

Insurance and Direct-Billing Receivables

If your clinic direct-bills extended health insurers through Jane, each submitted claim is a receivable until the insurer pays. Revenue should be recorded when the service is delivered, not when the insurer’s payment lands — otherwise your monthly income swings with payment timing rather than the work you actually did. Track outstanding claims so you can see what’s owed to you and follow up on anything that stalls.

How Wellspring Helps Jane App Clinics

Jane App is part of our daily workflow. We set up a clean monthly reconciliation between your Jane reports and your bank, capture Jane Payments processing fees correctly, code GST/HST so exempt services and taxable products are never confused, and handle the deferred-revenue and receivable adjustments that Jane surfaces but doesn’t post for you.

We work with Ontario clinics in particular. If your practice is in Ontario, see your profession’s accounting page — including chiropractic, physiotherapy, massage therapy, acupuncture, naturopathy, psychotherapy, and dietitians & nutritionists — or read our bookkeeping guide for wellness clinics.