Bookkeeping for Medical Practices
Medical Bookkeeping for Physicians and Specialists
Insurance payer mix reconciliation, physician compensation models, specialist contractor payments.
- AIPB Certified
- QuickBooks ProAdvisor
- Xero Partner
- US-based team
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A medical practice's books carry two problems most bookkeepers only understand in theory. The first is payer mix: private insurance, Medicare, Medicaid, and self-pay, each reimbursing differently and each landing in the bank account on its own schedule. The second is compensation. Physicians in a group practice aren't paid the same way twice, salary here, RVU-based production there, a percentage split somewhere else, and the books need to reflect all three without turning payroll into a monthly negotiation.
We work with solo physicians, small specialist groups, and multi-provider practices running everything from straight salary to full productivity-based compensation. What's consistent across all of it is the need for someone who can reconcile a payer mix accurately and run compensation calculations that hold up when a physician asks how their number was reached.
Once we're running the books, payer mix reconciles by category every month, compensation runs are documented and repeatable, and specialist contractors get paid and tracked correctly from the first invoice. Quarterly estimated tax for the physicians themselves stops being a guess based on last year's number.
Where medical practices bookkeeping actually helps
- My payer mix is a blur of insurance deposits that don't match what I billedReconciliation broken out by payer, private insurance, Medicare, Medicaid, self-pay, so deposits tie back to what was billed even with the reimbursement lag.
- Physicians in my group are paid three different ways and payroll gets complicated fastCompensation runs built for salary, RVU-based, and productivity models side by side, documented and repeatable each cycle.
- I bring in specialist contractors for coverage and I'm never sure I'm handling the 1099 side correctlySpecialist contractor payments tracked with W-9s on file, so 1099-NEC filing at year end is built from clean data, not reconstructed in January.
- My own quarterly estimated tax as a physician is basically a guess every quarterQuarterly estimated tax for physician compensation, whether salary or productivity-based, calculated from actual numbers each period, not carried over from last year.
- My practice software and accounting software live in two different worldsPractice management platform integrated with QuickBooks or Xero so financial data moves automatically instead of getting re-entered.
What's different about medical practices bookkeeping
- Insurance payer mix reconciliation across private insurance, Medicare, Medicaid, and self-pay
- Physician compensation models handled correctly, salary, RVU-based, or productivity split
- Specialist contractor payments tracked with W-9s collected before the first invoice
- Quarterly estimated tax calculated for physician compensation each period
- Practice management software integration with your accounting platform
- Monthly payer-mix and compensation reporting built into your financial statements
Why physician compensation trips up generalist bookkeepers
Most bookkeepers who haven't worked with a medical practice treat physician pay like standard payroll, one rate, run on a schedule. Medical practice compensation rarely works that way. A group might have one physician on straight salary, another on an RVU-based formula tied to production, and a third on a percentage split of collections. Each model needs its own calculation, its own documentation, and a way to explain the number if a physician asks how it was reached. Get this wrong and it stops being a bookkeeping error and starts being a conversation nobody in the practice wants to have.
The payer mix carries a similar complexity. A single visit might generate a private insurance payment at one rate, a Medicare payment at another, and a self-pay balance written down to a sliding scale. Reconciling that accurately, and being able to show which payer categories are actually supporting the practice, takes more than matching a deposit total to a bank statement. It takes a chart of accounts built around the payer categories from the start.
We build both into the setup at onboarding: compensation formulas documented for each model in use, payer categories built into the chart of accounts, specialist contractors tracked with W-9s on file before the first payment. The result is a monthly close that a physician can actually understand, and a year-end pack that reconciles cleanly for whoever handles the practice's tax filing.
What's included
- Bank and merchant account reconciliation, including payer deposits
- Payer mix categorization across private insurance, Medicare, Medicaid, and self-pay
- Physician compensation runs for salary, RVU-based, and productivity models
- Specialist contractor payment tracking and W-9 collection
- Quarterly estimated tax calculations for physician compensation
- Payroll for W-2 clinical and administrative staff
- Monthly profit and loss with payer-mix and compensation detail
- Year-end handover to your CPA or EA
Why medical practices and physicians pick us
We understand payer mix
Private insurance, Medicare, Medicaid, self-pay. Each reconciled as its own category so the practice can see which payer types actually support it.
Compensation, done by model
Salary, RVU-based, or productivity split, each calculated and documented in a way that holds up when a physician asks how the number was reached.
Specialist contractors, tracked cleanly
1099-NEC filing at year end built from data that was clean all year. W-9s collected before the first invoice clears.
Quarterly tax, not a guess
Physician quarterly estimated tax calculated from actual compensation each period, factoring in whichever model the practice runs.
Practice software, connected
Your practice management platform integrated with QuickBooks or Xero, so financial data moves through automatically.
Solo physician or multi-provider group
The same reconciliation discipline whether it is one provider or a group running several compensation models side by side.
Three medical practice shapes
One provider, straight salary, three payer types
Independent physician billing private insurance and Medicare, with a smaller Medicaid caseload. Compensation is straightforward but the payer mix reconciliation eats an evening a month.
What changes
- Payer mix reconciled monthly by category
- Quarterly estimated tax calculated each period
- Practice software connected to accounting
- Clean year-end pack for the CPA
How medical practice books typically run
In-house, part-time Office manager doing double duty | General bookkeeper Not specialized to payer mix | Medical practice plan (us) Built for payer mix and comp models | |
|---|---|---|---|
Payer mix reconciled by category | Partial | Partial | Yes |
Compensation runs documented by model | No | Partial | Yes |
Specialist contractor W-9s on file | Partial | Partial | Yes |
Physician quarterly tax calculated | No | Partial | Yes |
Practice software integrated | No | Partial | Yes |
Reviewed by an AIPB-certified bookkeeper | No | No | Yes |
How we price medical practices bookkeeping
Pricing for medical practice bookkeeping depends on the number of providers, how many compensation models the practice runs, and the complexity of the payer mix. A solo physician on straight salary costs less to run than a group with three compensation structures and a rotating list of specialist contractors.
Fill out the quote form and describe the practice, provider count, compensation approach, and payer mix. You'll get a written number back within one business day.
Related industries
What clients say
"Insurance reimbursements, private pay, sliding scale, three different rates for three payer types. It made my head hurt every month-end. They handle the reconciliation now, and the monthly P&L actually tells me how each payer type is performing. First time I have understood my own clinic finances."
"Associate dentist contracts and treatment plan revenue made our books look weirder than they actually were. Switching to them, the first thing they did was rebuild the chart of accounts properly. The financials suddenly made sense."
Medical Practices bookkeeping FAQ
Two things to remember
Every account is reconciled and kept tax-ready by an AIPB-certified bookkeeper. Every account is run inside the US. Those two anchors shape how we handle compliance for medical practices and physicians specifically.
Books that match the practice.
Books that match the practice. Tell us about your provider count and compensation model and we will quote the same day.