Medical practices have a billing cycle that differs from most small businesses. A patient receives care, insurance gets billed, insurance pays part of the claim, and the patient owes the remainder. The patient portion might be a copay collected at the visit, a deductible billed later, or coinsurance calculated after the claim processes. Tracking all of this requires understanding which system handles what.

Your practice management software handles the operational detail. Whether you use Kareo, AdvancedMD, athenahealth, or another platform, this is where claims get submitted, ERAs get processed, and patient statements get generated. The billing system knows which claim is pending with which payer, what insurance paid on each date of service, and what the patient still owes. Don’t try to replicate this detail in your accounting software.

QuickBooks or your accounting system holds the summary. Total revenue, total adjustments, total accounts receivable. When you record a deposit, you’re matching the bank activity to revenue categories, not tracking individual patient balances. Most practices sync daily or weekly deposits rather than individual payments.

Revenue should be recorded when you provide the service, not when you receive payment. This is accrual accounting and it’s the right approach for medical practices. When a patient visits, you record the expected revenue. When insurance pays less than billed, the difference becomes a contractual adjustment. When a patient balance becomes uncollectible, that’s a write-off.

Set up your chart of accounts to reflect how revenue actually flows. You need income accounts for services, separate accounts for contractual adjustments, and clear categories for patient write-offs and refunds. Some practices also separate revenue by service line or provider if they want that visibility in financial reports.

For deposits, insurance payments and patient payments should be easily identifiable. Insurance EFTs come with ERA files that show exactly which claims are being paid. Patient payments through credit card processors or payment portals arrive separately. Match these to the deposit entries in your books and categorize them correctly.

The monthly reconciliation is where everything comes together. Your accounts receivable in the accounting software should match the total aging from your practice management system. If they don’t tie out, something got recorded twice or skipped entirely. Either payments aren’t reducing receivables properly or charges aren’t flowing from the billing system. Catching this monthly keeps small discrepancies from becoming big problems.

Working with a bookkeeper familiar with LA County small businesses who understands medical billing workflows makes this easier. The mechanics aren’t complicated once you know which system owns which piece of information. Keep claim-level detail in your practice software and summary financials in your accounting system, and the two will work together instead of creating confusion.