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Affiliate Payout Runs and Reconciliation

Group due commissions into payout runs, complete PayPal or Wise payments or send Stripe transfers, reconcile results, and recover retryable failures.

Table of Contents

This page is for merchants paying affiliates. You pay affiliates through payout runs. A payout run groups eligible due commissions into payout records, then tracks whether each payout was exported, processed, marked paid, or sent back for remediation.

Core workflow

  1. Open Payouts.
  2. Choose New Payouts.
  3. In the New payouts window, review the eligible affiliates, their commission counts, and totals. An affiliate marked Missing payout details cannot be selected until they add payout details. With Stripe payouts, each affiliate instead shows how they’ll be paid, such as Stripe transfer or PayPal export (Stripe can’t pay them), or why they can’t be selected yet.
  4. Select the affiliates to include, then choose Create payouts. The optional Execute payouts immediately checkbox and Optional payment reference override field are on the same form.
  5. For PayPal or Wise, choose Export on the Payouts page, select the payouts, choose an export format (or leave Auto), choose Create export, then choose Download export from the export’s actions menu and complete payment outside AffiliateBase.
  6. For Stripe payouts, check Execute payouts immediately to send the Stripe transfers when you create the run, or send them later with Execute now on the payout run. Your available Stripe balance must cover the whole run. If it doesn’t, nothing is sent and AffiliateBase tells you how much to add.
  7. For PayPal or Wise, after the provider confirms payment, open the export’s actions menu and select Settle payouts. This immediately marks every payout in the export paid, with no confirmation step; keep the provider’s batch or transaction ID in your own records.
  8. Use Reconcile to review recent run health and fix unresolved states.

If your account pays through Stripe but Stripe payouts are turned off for it, New Payouts shows “Stripe payouts are turned off for this account” and Create payouts is disabled.

Only commissions in due state can be grouped into a new payout.

If a commission is voided (for example, by a refund) before its payout is submitted, AffiliateBase removes it from that payout. If it was the payout’s only commission, the payout is removed as well. A payout that Stripe definitely rejected and returned to due still counts as not submitted.

Once a payout has been exported or sent to Stripe, voids and refunds no longer change it. Instead, they create a negative adjustment (clawback) that is deducted from the affiliate’s future payouts. See Commissions and Fraud Review.

Payment behavior

  • If the account payout method is paypal, generate PayPal exports, pay affiliates in PayPal, and then mark or reconcile the payouts as paid.
  • If the account payout method is wise, generate Wise exports, pay affiliates in Wise, and then mark or reconcile the payouts as paid.
  • PayPal and Wise exports leave out payouts that already have a Stripe payment attempt or an externally recorded payment, so no affiliate is paid twice. In the other direction, AffiliateBase never submits an exported payout to Stripe.
  • Exports only include payouts with a positive amount.
  • If the account pays through Stripe (Stripe Connect), AffiliateBase sends one Stripe transfer per payout from your Stripe balance to the affiliate’s Stripe account. Before sending, it checks that your key works, the affiliate’s Stripe account is ready, and your available balance covers the payouts. A payout is marked paid when Stripe accepts its transfer. Affiliates that Stripe can’t pay are paid with their PayPal or Wise fallback through an export.
  • A Stripe payout that didn’t go through returns to due. Open it and choose Retry Stripe transfer after fixing the cause. If a transfer is still being confirmed, wait: AffiliateBase checks with Stripe before sending again, so nobody is paid twice. See Pay affiliates through Stripe.

Record a payment made outside AffiliateBase

Use Payouts -> Record external payment when you already paid an affiliate outside AffiliateBase and want the commissions marked paid. The form lists unpaid due commissions that are not yet in a payout. Select the commissions covered by one payment (one affiliate and one currency), enter the Payment reference from your payment provider or bank and the Actual payment date, choose Review payment, then choose Record payment on the confirmation step. This does not send money, and AffiliateBase does not verify the payment with the provider.

Payout statements

Every paid payout has a Download statement (PDF) button on its payout details. The statement shows the statement number, payment date, your business name, the affiliate’s name and email, the amount, the payment method, and each commission the payout covered with its total.

Affiliates download the same statement from their payout details in the affiliate portal. Customers on it appear the way the affiliate sees them: anonymous unless the campaign shows customer names and emails to affiliates.

A statement is proof of payment for the affiliate’s records. It is not a tax invoice, and it says so. Payouts that aren’t paid yet have no statement.

Reconciliation

Use Payouts -> Reconcile to open Payout Reconciliation. Set Lookback days (1 to 90) and choose Refresh to audit recent payout runs. The view shows evaluated runs, runs with issues, and an issue list with recommended remediation actions.

The reconciliation view helps you find:

  • runs with unpaid or failed payouts
  • payouts stuck in processing
  • missing recipient details
  • provider errors or payment references that need review

Typical remediation actions

  • Retry unpaid payouts
  • Review export results and payment references
  • Reset stuck processing payouts
  • Ask the affiliate to choose Continue in Stripe when Stripe needs more information from them
  • Add funds to your Stripe balance when a run or transfer reports a shortfall

For PayPal and Wise exports, do not mark a payout paid until the provider confirms the money was sent.

Partial provider success

If only some rows in a PayPal or Wise file were paid, do not select Settle payouts on the export. That marks every payout in it paid, including the failed rows. A downloaded export cannot be voided or split, so pay the failed rows directly in PayPal or Wise, then settle the export once every row is paid. See If Only Some Rows Were Paid.

Next steps