Medical bookkeeping brings financial activity and supporting records into an agreed review process. These ten tips identify questions about accounts, reimbursements, payroll and reports. Complete records and qualified review remain necessary; bookkeeping does not establish healthcare compliance or guarantee an audit outcome. For hands-on help, see our Accounting & Bookkeeping Services.
Table of Contents
1) Separate Practice & Personal Finances
Keep a dedicated operating account and credit card for the practice. Discuss reporting needs and separate legal structure questions through our Business Consulting.
2) Reconcile Bank & Merchant Deposits Monthly
Match EHR/merchant batch reports to bank deposits and adjust for fees/chargebacks. If you’re behind, our Business Tax Preparation team can help with cleanup and monthly closes.
3) Map Accounts to Medical Practice Activity
Use categories for provider payroll, supplies, lab fees, malpractice, rent, equipment leases, and EHR. We’ll design the right structure via consulting.
4) Track AR by Payer & Procedure
Track payer balances in approved practice systems and use appropriate financial summaries for reporting. Confirm compatibility and privacy controls before connecting systems or engaging Controller/CFO support.
5) Digitize Receipts & Keep HIPAA-Aware Workflows
Use access-controlled storage for receipts and financial records. Avoid including patient information in routine accounting files. Confirm privacy responsibilities and approved data handling before sharing practice data; tax representation does not provide healthcare compliance assurance.
6) Get Payroll & Provider Compensation Right
Review worker classification, compensation and payroll reporting requirements with the appropriate adviser. Agree on the processes and responsibilities included in our Payroll Support.
7) Watch Sales/Use Tax on Supplies & Retail
Practices that sell products may owe sales tax. Track nexus and file correctly with our Sales Tax Filing help.
8) Close Monthly: P&L, Balance Sheet, Cash Flow
Review gross margin by service line, payer mix, and overhead trends. For advanced analysis, consider our Outsourced CFO Services.
9) Plan Quarterly Estimates & Year-Round Tax Strategy
Coordinate write-offs, Section 179/bonus depreciation, and retirement plans. Explore our Tax Preparation for Personal and Business.
10) Document Medical Practice Review Procedures
Document procedures, approvals and access permissions. For an IRS notice, check the response deadline and discuss representation authorization and scope promptly. No adviser can guarantee resolution or the outcome of an audit.
Frequently Asked Questions (FAQs)
Which bookkeeping software works best for medical practices?
Confirm compatibility between your accounting software, EHR and any approved reporting connection. Do not assume a direct integration exists. Define what financial data may be shared, access controls and setup responsibilities before implementing a connection.
How do we manage payer reimbursements and denials?
Track payer balances and aging with the practice’s billing team. Billing specialists should evaluate denial codes and payer requirements. Bookkeeping or CFO reporting may support oversight, but does not guarantee reimbursement or replace medical billing and compliance expertise.
Can you help if we’re months behind on the books?
Yes—cleanup/catch-up gets you current, then we establish a monthly close. Start with Business Consulting and move into ongoing bookkeeping.
Need Bookkeeping Built for Medical & Dental?
Discuss the bookkeeping, payroll support, financial reporting and tax services your practice needs. Confirm the scope and any work requiring medical billing or healthcare compliance specialists. Schedule Consultation