What is Payment Reconciliation?

Payment reconciliation is the financial process of matching payments received from customers, marketplaces, and payment processors against the corresponding orders, invoices, and expected amounts in your accounting system. The goal is to confirm that every sale results in the correct payment being collected and recorded, identify discrepancies such as short payments, overpayments, duplicate charges, or missing payouts, and ensure that financial records accurately reflect the business’s revenue. For multichannel sellers, payment reconciliation is particularly complex because each sales channel has its own payment timing, fee structures, and payout schedules.

Why It Matters

Without systematic payment reconciliation, businesses operate with an unreliable picture of their financial health. Unreconciled transactions can hide significant problems: marketplace fees charged incorrectly, refunds not reflected in payouts, chargebacks deducted without notification, or currency conversion losses on international sales. These discrepancies may seem small individually but compound over thousands of transactions into material revenue leakage.

For multichannel sellers, the challenge is amplified by the diversity of payment flows. Amazon pays out biweekly with complex fee deductions. Shopify processes payments daily or on a rolling schedule. Wholesale customers pay on net-30 or net-60 terms. eBay, Walmart, and other marketplaces each have their own payout calendars and fee calculations. Reconciling all of these payment streams against orders requires either significant manual effort or automated matching systems that can handle the complexity.

How It Works

Payment reconciliation follows a systematic matching and exception-handling process:

• Data Collection: Payment data is gathered from all sources: bank statements, payment gateway reports (Stripe, PayPal, Square), marketplace payout reports (Amazon Seller Central, Shopify Payments), and accounts receivable records for B2B invoices. Each source provides transaction-level detail including amounts, dates, fees, and reference numbers.
• Transaction Matching: Each payment is matched to its corresponding order or invoice. Direct channel payments (credit card charges) are matched to individual orders by transaction ID. Marketplace payouts, which bundle many orders into a single deposit, must be broken down by order and reconciled against the expected payout after fees, refunds, and adjustments.
• Fee Verification: Marketplace fees, payment processing fees, shipping charge adjustments, and promotional discounts are verified against expected rates. Incorrect fees—which occur more frequently than most businesses realize—are flagged for dispute or recovery.
• Exception Handling: Unmatched transactions, amount discrepancies, and missing payments are isolated and investigated. Common exceptions include partial refunds not reflected in payouts, chargeback deductions, currency conversion differences, and timing differences between order date and payment settlement date.
• Recording and Reporting: Reconciled transactions are recorded in the accounting system with accurate revenue, fee, and net payout amounts. Reconciliation reports provide visibility into payment health, outstanding receivables, and fee trends across channels.

How Nventory Helps

Nventory simplifies payment reconciliation by centralizing order data from all sales channels in a single system. Every order includes complete financial details—sale price, taxes, shipping charges, discounts, and expected marketplace fees—making it straightforward to compare expected revenue against actual payouts. By providing a unified view of orders across channels alongside their financial data, Nventory reduces the manual effort needed to reconcile payments and helps businesses catch discrepancies before they compound into significant revenue loss.