--- title: "Payment processor & marketplace reconciliation for medical practices & clinics" description: "Payment processor & marketplace reconciliation for medical practices & clinics: merchant and marketplace reconciliation with A2X, Link My Books or Synder." url: https://ledgerbpo.com/industries/medical-practices/payment-processor-reconciliation/ updated: 2026-09-11 publisher: LedgerBPO (SS Support Network LLC) language: en-US --- # Payment processor & marketplace reconciliation for medical practices & clinics Stripe reconciliation for medical practices & clinics, and the same work for Square, Rectangle Health, CardConnect or the processor embedded in your patient portal, comes down to matching net payouts to gross patient payments. Patients pay copays at the desk, balances through the portal, and installments on card-on-file, and each processor batches those into deposits net of fees on its own schedule. - Since 2020 - US · UK · CA · AU - Named accountant plus backup - Your software, no lock-in [Book a billing audit](https://ledgerbpo.com/book-a-call/?topic=billing-audit) [Book a 20-minute call](https://ledgerbpo.com/book-a-call/) Updated September 2026 ## How it runs for medical practices and clinics Our ReconBot workflow pulls each payout report, ties it to a bank deposit and to the patient payment batch in the practice-management system, posts fees, refunds and chargebacks to their own accounts, and reconciles the processor balance to a clearing account at every close. ## What is payment processor reconciliation? Payment processor reconciliation is the work of proving that the money a processor or marketplace deposits equals your gross sales less its fees, refunds, chargebacks, reserves and adjustments for the same settlement period. Each payout is broken into its parts and posted so revenue, fees and sales tax are correct and the bank deposit matches to the cent. ## What we handle for medical practices and clinics - Match each processor payout to a bank deposit and the patient payment batch it settles - Reconcile front-desk terminal batches to the daily practice-management deposit report - Post processor fees, refunds and chargebacks separately from patient payments - Track card-on-file installment plans against patient balances each month - Reconcile the processor balance to the ledger clearing account at each close ## The KPI that matters here Every processor payout matched to a deposit and a patient batch within two business days, with fees posted separately. ## Medical practices compliance notes ### HIPAA Claims, remittances and patient statements are protected health information. We sign a BAA, staff are HIPAA-trained, access to your practice-management system is role-limited with MFA, and ledger entries carry claim or batch numbers rather than patient names or diagnoses. ### Payer rules and timely filing Every payer contract sets timely-filing limits, appeal windows, coordination-of-benefits rules and refund procedures. Medicare allows 12 months from the date of service to file; many commercial payers allow less. We log deadlines per payer so unpaid claims are worked before they age out. ### Overpayment refunds Identified Medicare and Medicaid overpayments must be reported and returned within 60 days of identification under the Affordable Care Act. We age credit balances by payer, prepare refund batches for your approval, and document the dates so the practice can show it acted in time. ### Patient credit balances and unclaimed property Patient overpayments that go unrefunded may become reportable unclaimed property under state law after a dormancy period. We list patient credits monthly, prepare refunds for your approval, and keep records that support any state filing your counsel advises. ## Medical practices software we work in - [Kareo (Tebra)](https://ledgerbpo.com/software/kareo-tebra/) - [AdvancedMD](https://ledgerbpo.com/software/advancedmd/) - [QuickBooks Online](https://ledgerbpo.com/software/quickbooks-online/) - [Gusto](https://ledgerbpo.com/software/gusto/) - [Bill.com](https://ledgerbpo.com/software/bill-com/) - [Stripe](https://ledgerbpo.com/software/stripe/) - athenahealth - eClinicalWorks - [All 50 platforms](https://ledgerbpo.com/software/) ## More for medical practices and clinics Other services for medical practices - [Bookkeeping](https://ledgerbpo.com/industries/medical-practices/bookkeeping/) - [Invoicing and billing](https://ledgerbpo.com/industries/medical-practices/invoicing-and-billing/) - [Accounts receivable](https://ledgerbpo.com/industries/medical-practices/accounts-receivable/) - [Accounts payable](https://ledgerbpo.com/industries/medical-practices/accounts-payable/) - [Bank reconciliation](https://ledgerbpo.com/industries/medical-practices/bank-reconciliation/) - [Month-end close](https://ledgerbpo.com/industries/medical-practices/month-end-close/) - [All medical practices services](https://ledgerbpo.com/industries/medical-practices/) Payment processor reconciliation in other industries - [Marketing agencies & consultancies](https://ledgerbpo.com/industries/agencies/payment-processor-reconciliation/) - [Auto repair shops & dealerships](https://ledgerbpo.com/industries/auto/payment-processor-reconciliation/) - [Behavioral health practices](https://ledgerbpo.com/industries/behavioral-health/payment-processor-reconciliation/) - [Daycares, schools & education](https://ledgerbpo.com/industries/childcare-education/payment-processor-reconciliation/) - [The full payment processor reconciliation page](https://ledgerbpo.com/services/payment-processor-reconciliation/) ## Frequently asked questions ### Why does the processor deposit never match the day's patient payments? The processor deducts fees per transaction, batches several days together, and subtracts refunds and disputed charges from later payouts. A single deposit can therefore represent parts of three days minus a refund from last week. Matching the payout report line by line is the only way the bank, the patient ledger and the fee expense will agree. ### How do you handle patient refunds issued through the processor? A refund run through the terminal or portal reduces a later payout. We record the refund against the patient's account in the practice-management system, match the reduction on the payout report, and confirm it agrees to the bank. Refunds paid by check follow the refund register instead, so the two routes are never confused or double-counted. ### Can you reconcile installment plans on card-on-file? Yes. Each scheduled charge is matched to the patient's balance and to the payout it appears in, so the plan's remaining balance in the practice-management system agrees with what has actually cleared the bank. Failed charges are flagged for the office to follow up, and the practice's own policy governs how the patient is contacted. Next step ## Books closed. Invoices paid. Every month. Tell us what is going on with your books or billing. You will hear from a named person within 1 business day, with a custom quote and a plan for the first close. - Reply from a named person within 1 business day - No setup fee, month-to-month - Your software, your data, no lock-in Start with a custom quote [Book a billing audit](https://ledgerbpo.com/book-a-call/?topic=billing-audit) [Book a 20-minute call](https://ledgerbpo.com/book-a-call/) Or call [+1-657-777-0006](tel:+16577770006) during US, UK or Australian business hours. --- Source: https://ledgerbpo.com/industries/medical-practices/payment-processor-reconciliation/ · Contact: https://ledgerbpo.com/contact/ · Full site map for agents: https://ledgerbpo.com/llms.txt