--- title: "Accounting software setup & migration for medical practices & clinics" description: "Accounting software setup & migration for medical practices & clinics: quickBooks, Xero, Zoho Books and Sage setup, plus migration from Bench, Wave." url: https://ledgerbpo.com/industries/medical-practices/accounting-software-setup/ updated: 2026-09-11 publisher: LedgerBPO (SS Support Network LLC) language: en-US --- # Accounting software setup & migration for medical practices & clinics QuickBooks setup for medical practices & clinics is mostly about designing accounts that mirror the practice-management system and keeping patient information out of the ledger. We build a chart with gross charges, contractual adjustments and net patient revenue by payer class, cost of services for drugs and vaccines, provider compensation by provider, and location classes. - 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 Clearing accounts are set up for claims and for the card processor, the deposit report from Kareo/Tebra or AdvancedMD is mapped to those accounts, payroll departments are mapped by provider and location, and bank-feed rules are configured. Migrations from QuickBooks Desktop or a spreadsheet include opening balances and a parallel month. ## What is accounting software setup and migration? Accounting software setup is the configuration of a new ledger: chart of accounts, tax codes, bank feeds, items, users and apps. Migration is moving existing books from another platform or spreadsheet into that ledger so history, open items and balances carry across. Both end with a file that agrees to the old records and is ready for live posting. ## What we handle for medical practices and clinics - Design a chart with gross charges, contractual adjustments and net revenue by payer class - Set up classes for locations and provider tags for compensation reporting - Map practice-management deposit reports to clearing and revenue accounts - Configure payroll department mapping and bank-feed rules for recurring items - Migrate opening balances and open items with one parallel month before cut-over ## The KPI that matters here Cut-over completed with opening balances tied to the prior system and the first close delivered on schedule. ## 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/) Software setup and migration in other industries - [Marketing agencies & consultancies](https://ledgerbpo.com/industries/agencies/accounting-software-setup/) - [Auto repair shops & dealerships](https://ledgerbpo.com/industries/auto/accounting-software-setup/) - [Behavioral health practices](https://ledgerbpo.com/industries/behavioral-health/accounting-software-setup/) - [Daycares, schools & education](https://ledgerbpo.com/industries/childcare-education/accounting-software-setup/) - [The full software setup and migration page](https://ledgerbpo.com/services/accounting-software-setup/) ## Frequently asked questions ### How should a medical practice's chart of accounts be organized? Gross charges, contractual adjustments and net patient revenue by payer class; cost of services for drugs, vaccines and lab; provider compensation and malpractice by provider; staff cost by department; and overhead by category. Add clearing accounts for claims and for the card processor, and classes for locations. This structure yields provider and location reporting straight from the ledger. ### Does the practice-management system sync with QuickBooks Online? Some systems export a daily or monthly deposit and adjustment summary that can be imported, and a few offer direct integrations. We recommend posting summaries rather than claim-level detail, so patient information stays in the practice-management system. Where a sync exists we configure and reconcile it; where it does not we post from the reports on a fixed schedule. ### Should we keep patient names out of the accounting file? Yes. The general ledger does not need patient names, diagnoses or dates of service; it needs totals by payer class, batch numbers and dates. Keeping protected health information out of QuickBooks Online or Xero reduces the number of systems covered by your HIPAA program and makes it safer to share the books with your CPA, lender or a buyer. 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/accounting-software-setup/ · Contact: https://ledgerbpo.com/contact/ · Full site map for agents: https://ledgerbpo.com/llms.txt