Bookkeeping for therapy practices on SimplePractice, TherapyNotes and Jane

The short answer

SimplePractice, TherapyNotes and Jane each run scheduling, notes, billing and client payments well for therapy and behavioral-health practices. None of them is a full general ledger. Practices still need QuickBooks or similar for the P&L, balance sheet, tax reporting and owner draws, and the bookkeeping job is the same on all three: match bank deposits to the EHR's payment and income reports, record merchant fees and insurance adjustments correctly, and keep client-level detail out of the accounting file.

The table below shows where the three actually differ. It's part of our dental and therapy practice bookkeeping guide, and pairs with our other EHR spokes in this series.

Quick reference

SimplePractice: what the books need

SimplePractice handles client invoicing, insurance claims and online payments through a partnership with Stripe. SimplePractice's own support documentation confirms the exact fee: "the integration fee for online payments is 3.15% + $0.30 for each successful transaction," whether the card is charged at the time of service or stored for later use (SimplePractice). The Billing hub shows card transactions with gross charge, fee and net amounts, income reports break out client payments, insurance payments, card fees and net income, and an annual financial activity report rolls up Stripe processing expenses for the year. Payments export in a QuickBooks-oriented format or as CSV.

There's no full real-time ledger sync that replaces bookkeeping. The practical approach is to keep PHI and client-level detail inside SimplePractice and post summarized income and deposits into QuickBooks, often through a clearing or undeposited-funds account, so bank deposits that arrive net of Stripe fees can be matched cleanly. Book every bank deposit as "therapy income" at the gross session amount instead, and the fees disappear while income gets overstated.

TherapyNotes: what the books need

TherapyNotes combines documentation, electronic claims, assisted ERA posting, aging reports and integrated card processing. Client and insurance payments post directly to the client ledger, and TherapyNotes's own help center confirms the assisted ERA feature in detail: it scans the remittance, pulls payer and claim information automatically, detects copay, coinsurance and deductibles, and guides the user through posting the payment (TherapyNotes).

Card processing itself works differently here than on SimplePractice or Jane, and this is the one real correction to make to how this platform usually gets described: TherapyNotes' card payments run through a separate merchant services partner, CardConnect (now branded CardPointe after an acquisition by First Data), not through a Stripe-style integrated net-of-fee payout. TherapyNotes' own documentation confirms that "payment processing fees are taken out separately from TherapyNotes, and are withdrawn directly from your bank account at the start of each new month" (TherapyNotes), rather than being deducted from each individual transaction before it reaches the bank. That means a card payment usually hits the bank at its full amount, and the fee shows up later as a separate monthly debit, a different shape of risk than a net payout: if the bookkeeper isn't specifically watching for that monthly merchant withdrawal, the fee can be missed entirely rather than merely buried inside a netted deposit. TherapyNotes doesn't publish one flat percentage the way SimplePractice does; rates run through the merchant account and vary by practice.

Bookkeepers typically pull TherapyNotes' payment reports for a day or period and build summary entries in QuickBooks rather than importing every client name. The common trap is still real, just shaped differently: TherapyNotes shows the full session fee and the full card payment; if the bookkeeper only matches the bank's card deposits without separately tracking the monthly CardConnect withdrawal, both the gross-versus-adjusted revenue and the fee expense end up wrong.

Jane: what the books need

Jane is explicit about this, in its own words: "while Jane doesn't directly integrate with any accounting system, most of Jane's financial reporting is exportable to Excel, which can then be imported to your accounting software" (Jane's Guide). The Sales report exports as a CSV formatted to be compatible with QuickBooks or Xero import requirements, and Jane publishes dedicated walkthroughs for transferring that data into QuickBooks Online and Xero specifically. For Jane Payments users, processing fees show up as a negative line item directly on the report, and fee detail is also available separately on the Jane Payments Transactions report.

Jane Payments deposits hit the bank net of processing fees, and the payout and transaction reports are what the bookkeeper reconciles against the bank. Clinics either import sales detail, watching QuickBooks' invoice-import limits, or post a period summary journal for revenue, tax where applicable, and fees, then clear the bank deposits. Packages, gift cards and prepaid credits need deferred-revenue treatment when cash arrives before services are delivered, one more reason the EHR alone isn't the books.

What users say

SimplePractice runs 4.1 out of 5 on G2 across 125 to 128 reviews and 4.6 out of 5 on Capterra across roughly 2,820 reviews. TherapyNotes runs higher on both: 4.4 out of 5 on G2 across around 97 reviews, and 4.7 out of 5 on Capterra across roughly 960 reviews, with its support team drawing specific, repeated praise. Jane sits highest of the three on Capterra, 4.8 out of 5 across roughly 510 reviews, though its G2 sample is thin, 4.0 out of 5 across just 16 reviews, so treat that one figure as a weaker signal than the other two. None of the three draws much accounting-specific commentary; reviewers mostly weigh in on clinical workflow, scheduling and client experience.

Worked example: deposits that tie, income that does not

A solo or small group practice posts the following for one week, and sees the following bank activity for the same window:

If the bookkeeper only records the $5,955 as "Therapy income," gross charges never appear correctly, the $1,260 in adjustments never hits the P&L, the $195 in merchant fees never hits expenses, and QuickBooks income stops matching any of the three EHRs' own income reports. The bank reconciliation still clears.

On SimplePractice and Jane, that $195 in fees is already netted out of the payout shown above, so it's invisible unless the bookkeeper pulls the income or transaction report. On TherapyNotes, the mechanism is different: card payments typically arrive at their full amount, and the $195 shows up later as part of a separate monthly withdrawal from the merchant account. Miss that monthly debit entirely and the fee never hits the books at all, which is arguably an easier mistake to make than under-recording a fee that's already buried in a netted deposit.

Correct treatment uses each platform's own income or payment report, plus fee detail, to post revenue and adjustments, routes payments through clearing where needed, and matches the actual net deposits, or for TherapyNotes, the actual gross card deposits plus the separate monthly fee withdrawal.

Questions to ask before you choose

How Numetix works with these platforms

We sit alongside SimplePractice, TherapyNotes or Jane. AI categorizes bank activity against the EHR's payment, income and payout reports, and tracks fee mechanisms specific to each platform, including TherapyNotes' separate monthly merchant withdrawal. A CPA-overseen team owns deposit matching, fee and write-off classification, and the monthly close, so QuickBooks reflects true collections and cash without moving client names or clinical detail into the ledger.

A practical first step: send us a recent income or payment report from your EHR, a card or payouts export if you use integrated processing, and two weeks of bank activity. We'll show you the exact entries and the gaps. Book 30 minutes with our team. More on how Numetix serves therapy and behavioral-health practices.

Frequently asked questions

Do any of these EHRs replace QuickBooks? No. They're practice management and billing systems. QuickBooks or an equivalent remains the place for financial statements, tax, payroll and non-clinical expenses.

Is there a native QuickBooks sync on any of the three? No. SimplePractice offers payment exports usable with QuickBooks and detailed fee reporting; TherapyNotes is typically handled with summary entries built from payment reports; Jane states plainly that it has no direct accounting integration and provides CSV exports instead.

Does TherapyNotes deduct card fees from each payment the way SimplePractice does? No, and this is a real difference, not a minor detail. TherapyNotes' card processing runs through a separate merchant services partner, and fees are withdrawn from the bank once a month, not deducted from each individual transaction. A card payment typically hits the bank at its full amount, with the fee arriving later as its own line.

Where do merchant fees belong? As an expense, or a clearly labeled reduction of the deposit, never as invisible shrinkage of income. All three platforms surface fee information somewhere, but it has to be booked deliberately, and on TherapyNotes specifically, watched for as a separate monthly debit.

Should client A/R live in QuickBooks? Most therapy practices keep detailed client and insurance balances only in the EHR and use cash-basis summaries in QuickBooks. That reduces PHI exposure and keeps the ledger usable.

What reports should the bookkeeper request? SimplePractice: the income report, card transactions and payouts, and the annual financial activity report when needed. TherapyNotes: payment and income or collection reports for the period, ERA or payment-posting detail if insurance-heavy, and the monthly merchant-services statement for the fee withdrawal. Jane: the Sales report, the Transactions or Daily Transactions report, and Jane Payments payout information.

Can a third-party connector eliminate the bookkeeper? It can reduce keying. Someone still has to confirm deposits match, fees and adjustments are classified correctly, and the month closes cleanly.