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Best Practices for Payment Reconciliation

Emily McClendon avatar
Written by Emily McClendon
Updated over a week ago

Keeping your payment records consistent and accurate helps your practice save time, prevent errors, and simplify reporting. Follow these best practices to ensure your Practice by Numbers (PbN) Payments and Practice Management System (PMS) stay perfectly in sync.


1. Set a Consistent Cut-Off Time

Choose a specific daily cut-off time for recording payments in your PMS.
Any payments received after that time should be added to the next business day’s batch.

Having a clear cut-off ensures your payment records are accurate and time-bound.


Tip: Align the same cut-off time across your payment processor and PMS to avoid discrepancies.

Note: PbN payment terminals can also be configured to close out at a specific time each day automatically. To enable or adjust this setting, please contact PbN Support.


2. Use Daily Batch Processing

Enable daily batch processing with your payment processor to group transactions together. Batching consolidates all payments for the day into one report, making reconciliation faster and easier.

Ensure your batch close-out time aligns with your PMS cut-off time for consistency.


3. Reconcile Payments Daily

At the end of each business day, compare the totals in your PMS with reports from your payment processor or PbN Payments.


If any payments come in after hours, include them in the next day’s batch.

Reconciling daily helps you catch small discrepancies early before they turn into bigger issues.


4. Export the Payments Page

Within Practice by Numbers, you can export your Payments page to simplify reconciliation.

Use filters to view payments by date range, payment method, status, or provider before exporting.

You can then use the exported file to compare with batch reports from your PMS or processor.

Tip: Exporting to Excel or Google Sheets makes it easy to identify mismatches quickly.


5. Keep Clear and Organized Records

Maintain organized logs for each batch and transaction. Create labeled folders or PMS notes for quick reference and flag any mismatches with notes explaining the reason.


6. Automate Where Possible

If your PMS is integrated with PbN Payments, enable automated syncing.

Automation minimizes manual entry, reduces human error, and ensures your records update in real time.


7. Have a Plan for Discrepancies

Establish a simple process for investigating and resolving payment discrepancies.
Include steps such as checking transaction IDs, timestamps, and staff notes. Assign one team member to handle flagged items to keep records consistent.


8. Maintain Audit Trails

Ensure your systems keep an audit trail of all payment activity. Audit logs make it easy to track any transaction, prepare for tax season, or resolve disputes.


9. Train Your Team

Make sure everyone who handles payments understands the reconciliation process.
Include this training during onboarding and review it regularly to maintain consistency and accuracy.


10. Protect Payment Data

Restrict access to payment systems to authorized users only and ensure your software uses encryption and security best practices.

Safeguarding sensitive information keeps your patients and your business protected.


How This Helps Your Practice

Following these best practices ensures smoother operations between your PMS and Practice by Numbers:

  • Faster Month-End Close: Clean daily records make reporting effortless.

  • Less Manual Work: Automated syncing minimizes data entry.

  • Improved Accuracy: Prevents double payments, missed charges, and reporting errors.

  • Simpler Refunds & Audits: Clear records streamline patient refunds and financial reviews.

  • Better Team Alignment: Everyone works from the same accurate data.

By reconciling payments regularly, your practice can save time, reduce costly errors, and maintain complete confidence in your financial data.

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