Payments: Record, Reconcile, and Process Refunds

Payments: Record, Reconcile & Refunds

The Payments module ensures every payment received is correctly matched to an invoice, every discrepancy is flagged for review, and every refund is processed through an auditable workflow. This guide covers three essential operations: recording a manual payment, reconciling payment status, and processing refunds or credits.

1. Recording a Manual Payment

Manual payment recording is used when a client pays by bank transfer, cash, cheque, or any offline method that does not trigger an automatic gateway callback. Every manual payment must be recorded promptly to keep invoice statuses accurate.

1. Open the invoice: Navigate to Invoices, find the relevant invoice by client name, invoice number, or date, and open the invoice detail view.
2. Click Record Payment: The payment entry form opens. It pre-fills the outstanding amount — adjust this if it is a partial payment.
3. Enter payment date: Use the actual date the funds were received (e.g. the bank settlement date), not today's date if different. This is important for reconciliation and period-accurate financial reports.
4. Select payment method: Choose from the configured payment methods (Bank Transfer, Cash, Cheque, Stripe, etc.). If a method is missing, ask your admin to add it under Setup > Finance > Payment Methods.
5. Transaction reference: Enter the bank reference, cheque number, or gateway transaction ID. This is the key identifier for reconciliation — do not leave it blank.
6. Internal note: Add any relevant context — e.g. "Client paid via BACS on 2026-04-05, ref: PAY-2254". This note is visible to finance staff only and is not shown to the client.
7. Click Save. The invoice status automatically updates to Paid (if fully paid) or Partially Paid. A payment record appears in the invoice timeline.

2. Reconciling Payment Status

Reconciliation means matching your CRM payment records against your bank statements or payment gateway reports to ensure every payment is accounted for accurately. Run this process weekly at minimum.

1. Export the payment report: Navigate to Reports > Payments and export paid and partially paid invoices for the period being reconciled. Filter by date range, currency, and payment method as needed.
2. Compare with bank/gateway records: Open your bank statement or gateway dashboard (e.g. Stripe, PayPal) and match each transaction by reference number and amount.
3. Verify amounts and currency: Confirm the amount recorded in the CRM matches the net amount received after any gateway fees. Note: gateway fees should be tracked separately and not deducted from the invoice payment amount in the CRM.
4. Flag discrepancies: For any payment where the CRM amount does not match the bank record, open the payment record in the CRM and add an internal note marking it for finance review. Use a tag or status if your workflow supports it.
5. Update communication log: If a client has queried a payment, update the invoice notes and add a client-visible note confirming payment receipt and any reference details they may need for their own records.

3. Processing a Refund or Credit

Refunds are financial reversals and must follow your business's approval process. Never process a refund without confirming the original payment exists and the refund has been authorised.

1. Verify eligibility: Open the invoice or payment record and confirm the payment was received and is in a refundable state. Check your refund policy for applicable windows (e.g. within 30 days of payment).
2. Obtain authorisation: Confirm the refund has been approved by the appropriate team lead or finance manager. Document the approval in the invoice notes before proceeding.
3. Initiate the refund: From the payment record, click Refund or follow your configured refund workflow. For gateway-processed payments (Stripe, etc.), the refund can be initiated directly from the CRM if the gateway supports it. For manual payments, process the refund via your bank and then record it in the CRM.
4. Enter refund amount and reason: Specify whether it is a full or partial refund and enter a clear reason code (e.g. Duplicate Charge, Service Not Delivered, Client Cancellation within Policy). This reason is stored for audit purposes.
5. Confirm the outcome: For gateway refunds, wait for the gateway confirmation callback and verify the refund status updates in the payment record. For manual refunds, record confirmation of the outgoing bank transfer reference.
6. Notify the client: Send a refund confirmation using a communications template. Update the invoice status to Refunded or Partially Refunded as appropriate.

Common Issues

Related Articles

• Invoices: Create, Send & Track
• Clients: Profile, Contacts & Billing Setup
• Workflow: Invoices, Payments & Refunds
• Reports: Pipeline, Revenue & Performance