Payment Reconciliation Automation Overview Payment reconciliation matches what your payment processors (Stripe, PayPal, Shopify Payments) say they collected against what your accounting system recorded and what your bank actually received. Discrepancies arise from processor fees, refunds, chargebacks, rolling reserves, and currency conversion — none of which are automatically journaled in most ecommerce setups. Manual reconciliation does not scale beyond a few hundred transactions per day. For most merchants, automated reconciliation is solved by connecting your ecommerce platform to your acc…