Bookkeeping & Billing for Medical Practices & Clinics

Bookkeeping for medical practices and clinics: how LedgerBPO runs it

Bookkeeping for medical practices & clinics means tying the practice-management system to the general ledger: charges, ERA and EOB postings, contractual adjustments, patient payments at the front desk and through the portal, refunds, and physician compensation. LedgerBPO assigns a named, HIPAA-trained accountant who works from your Kareo/Tebra or AdvancedMD reports inside your own QuickBooks Online file, under a signed BAA.
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What we handle

Bookkeeping for medical practices & clinics means tying the practice-management system to the general ledger: charges, ERA and EOB postings, contractual adjustments, patient payments at the front desk and through the portal, refunds, and physician compensation. LedgerBPO assigns a named, HIPAA-trained accountant who works from your Kareo/Tebra or AdvancedMD reports inside your own QuickBooks Online file, under a signed BAA.
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Billing and books together

Practice-management deposits reconciled to bank and ERA remittances every month
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Reconciled every month

Patient balances, credit balances and refunds tracked so nothing is owed twice
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What you see

One HIPAA-trained team for claims follow-up and month-end financials
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A named accountant, a backup and a team lead

Inside your own software, on a fixed close calendar, with a reply from a person within 1 business day. Call +1-657-777-0006 or start a quote.
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Bookkeeping for medical practices and clinics: how LedgerBPO runs it36 seconds · captions on · no audio

Updated September 2026 · Reviewed by Nimra Khalid

Medical practices accounting challenges

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Patients now owe a bigger share
The average deductible for single employer coverage reached $1,787 in 2024 (KFF Employer Health Benefits Survey). More of every visit is collected from the patient after the ERA arrives, which means statements, portal payments and card-on-file must all reconcile to the practice-management ledger.
02
Payers pay on their own clock
Medicare holds electronic claims for a 14-day payment floor and commercial payers each follow their own contracted timelines, so a practice with six payers sees cash arrive in a dozen separate rhythms. Without ERA-level posting, a $40,000 deposit is just a number that may or may not be right.
03
Credit balances are a liability, not income
Overpayments from patients and payers accumulate quietly in the practice-management system, and identified Medicare and Medicaid overpayments must be reported and returned within 60 days under Section 6402(a) of the Affordable Care Act. Unclaimed patient credits also fall under state unclaimed-property rules.
04
Physician compensation depends on clean data
Many groups pay physicians on collections or wRVUs, so a posting error in the practice-management system changes someone's paycheck. Compensation formulas need collections by provider that tie to the bank, not to a report that was never reconciled.
05
One outage can stall cash for weeks
The February 2024 cyberattack on Change Healthcare halted claims and remittances for a large share of US practices for weeks (AMA survey, April 2024). Practices without a claims-clearing reconciliation could not say how much revenue was stuck, which made bridge financing harder to arrange.

What we handle for medical practices and clinics

Practice-management to ledger tie-out

Charges, adjustments, payments and refunds from Kareo/Tebra, AdvancedMD or athenahealth are posted to the ledger and the deposit report is tied to the bank every month.

ERA and EOB posting under a BAA

HIPAA-trained agents post 835 remittances and paper EOBs by claim, record contractual adjustments and denials by reason, and follow up on unpaid claims.

Patient collections and statements

Statements, portal payments and card-on-file receipts are reconciled, and courteous reminder calls go out under your practice's name through BillingLine.

Credit-balance and refund control

Patient and payer credit balances are aged, refunds are prepared for your approval, and identified overpayments are tracked against the 60-day rule.

Provider-level revenue and compensation

Collections by provider tie to the bank so wRVU or collections-based compensation is calculated from reconciled numbers.

Month-end close with a second reviewer

Bank, card, payroll, clearing and refund accounts are reconciled and reviewed before financials are released by the fifth business day.

Medical practices software we work in

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.

KPIs we report

KPI	Why it matters
Days from visit to claim submission	Charge lag is the earliest, most controllable source of slow cash in a practice.
ERA posted within 2 business days of deposit	Until the remittance is posted, the deposit cannot be tied to claims or to patient balances.
Days in accounts receivable by payer	A blended number hides the one payer whose claims are quietly aging out.
Patient responsibility collected at time of service	Copays and known deductibles collected at check-in cost far less to collect than statements sent later.
Credit balances older than 60 days	This is both a refund obligation and a signal that posting or coordination of benefits needs attention.

Services for medical practices and clinics

Frequently asked questions

What does bookkeeping for a medical practice include?

It includes tying your practice-management system's charges, adjustments, payments and refunds to the general ledger, reconciling ERA and patient payments to the bank, aging and refunding credit balances, booking payroll and physician compensation, coding vendor bills, and reconciling every account monthly. You receive a P&L by provider or location and an aging by payer each month.

Do you work in Kareo/Tebra, AdvancedMD or athenahealth?

Yes. We post and reconcile inside the practice-management system your practice already uses, and we carry the totals into QuickBooks Online or Xero. We work from the system's deposit, adjustment and aging reports, so the practice-management aging and the balance-sheet receivable agree at every close. We do not ask you to change systems.

Can you handle claims follow-up as well as the books?

Yes. Our HIPAA-trained billing agents post remittances, work denials and follow up on unpaid claims under a signed BAA, and the same team reconciles those results to the ledger. One team on both sides means the number on the aging is the number on the balance sheet, which is where most practices lose confidence in their reports.

How do you protect patient information?

We sign a business associate agreement before any access is granted, staff are HIPAA-trained, and access is role-limited with MFA. Ledger memos carry claim and batch numbers rather than names or diagnoses, and reports move through your systems or our LedgerDesk portal rather than email attachments. Access logs are available on request.

How do you calculate physician compensation?

We apply the formula your partnership agreement defines, whether it is collections-based, wRVU-based or a hybrid, using collections by provider that have been reconciled to the bank and wRVU data from your practice-management system. The calculation is documented and reviewed by a second accountant before it reaches the partners. We do not advise on the formula itself.

What does bookkeeping for a medical practice cost?

Pricing depends on volume and scope, so we send a custom quote within 1 business day. For reference, US outsourced bookkeeping typically runs $150 to $1,600 per month (indinero, 2026). Practices that add remittance posting, refund control and provider-level compensation reporting fall toward the upper part of that range because of the transaction volume.

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Bookkeeping and billing for medical practices & clinics