The money Shopify deposits in your bank almost never equals your gross sales for the period — fees, refunds, chargebacks, holds, and timing differences all sit in between. If you're not reconciling payouts against your accounting ledger, small discrepancies accumulate into real, unnoticed revenue leakage and a finance close that drags on for days.
For each payout, match the deposited amount to the sum of its underlying transactions minus fees and refunds, and confirm that total lands in your accounting ledger. Flag any payout where the math doesn't reconcile within a small tolerance — that gap is where unnoticed fees, double-refunds, or missing entries hide. Done continuously instead of once a month, reconciliation stops being a quarter-end fire drill and becomes a background check that surfaces leakage while it's still small enough to chase down.