Payment Reconciliation Checklist

Export the payout report from Shopify Admin → Finances → Payouts for the full reconciliation period. Use the per-transaction CSV (not just the summary) so you can match individual orders, fees, and refunds against the bank deposit. Confirm the date range matches your accounting close cutoff.

Pull the balance transaction export from Stripe (Reports → Balance) and the activity download from PayPal (Activity → All Reports → Transactions). Both group by payout / deposit batch — keep that grouping; it's the unit you'll match to bank entries.

Retrieve the Amazon Date Range Settlement Report (Seller Central → Reports → Payments), eBay financial summary, and Walmart settlement report for any active marketplaces. Marketplace facilitator sales tax is collected and remitted by the platform — note it separately so it doesn't double-count as revenue.

Download statements (or live bank feed export) for every operating account that receives payout deposits. If gateway payouts route to multiple accounts (e.g., Stripe to checking, Amazon to a separate sub-account), pull each one.

Tie each Stripe / PayPal / Shopify Payments / Amazon payout batch to a bank deposit line by amount and arrival date. Watch for the 1-2 business-day lag between payout creation and bank arrival, and for weekend/holiday deposit consolidation.

For each charge in the gateway export, confirm a matching order in Shopify / Amazon. Common gotcha: gift card redemptions and store credit reduce the charged amount — the order total won't equal the gateway charge in those cases.

Cross-check Stripe / Shopify Payments / PayPal fee deductions against your contracted rate (e.g., 2.9% + $0.30 domestic, higher for AmEx and international). Rate creep on cross-border, currency conversion, and Shop Pay Installments fees is a frequent silent margin drain.

Identify charges captured before period close but paid out after — these belong on the books in the close period as a payment-processor receivable, not as cash. Amazon's reserved balance (Account Level Reserve) and Stripe's pending balance both fall in this bucket.

Most unmatched items are timing — captured on day 30, deposited on day 32. Confirm the order's authorize and capture timestamps in the gateway, then move the item to the next period's reconciliation queue rather than treating it as a true discrepancy.

For amounts that aren't timing differences — missing payouts, fee miscalculations, duplicate charges — file a case with the gateway through Stripe Support, Shopify Help Center, or PayPal Resolution Center. Reference the specific charge ID and payout ID; vague tickets bounce around for days.

Submit evidence packages for each open dispute: order confirmation, AVS/CVV match, shipping carrier proof of delivery with signature, customer communication thread. Per-issuer deadlines vary (Visa CE 3.0, Mastercard, Amex) but Stripe / Shopify shows the next-action deadline on each dispute. Missing the deadline forfeits the case.

Book corrections in QuickBooks Online, Xero, or NetSuite — fee true-ups to processor-fee expense, write-offs of unrecoverable chargebacks, and reclasses between sales/refunds and payment-processor clearing. A2X or Bookkeep can automate the marketplace summary journal if you're using one.

Build the period summary: gross sales by channel, processor fees, refunds, chargebacks, net deposits, and ending receivable balance per gateway. Reconcile the receivable balance to each gateway's pending-payout figure as of period end.

Compute disputes / total transactions for the period. Visa's monitoring threshold is 0.9% (VDMP) and 1.8% (VFMP); a sustained climb past 0.65% is a signal to tighten fraud rules in Shopify, Stripe Radar, or Signifyd before the card networks intervene.

Confirm that tax collected and remitted by Amazon, eBay, Walmart, and Etsy is recorded as a pass-through, not as revenue. Direct-channel (Shopify) tax stays your liability — tie it to the Avalara / TaxJar / Anrok report for the matching period.