Reconciling WooPayments payouts in QuickBooks Desktop

Your bank shows one line from WooPayments: 337.79. Your store shows two orders, 264.54 and 120.00, and a refund of 35.00. Nothing on either side says 337.79, and that is where most store bookkeeping goes wrong.

Why the numbers never line up

A payout is not a sum of orders. WooPayments collects the full amount from each customer, keeps its card fee, takes back any refunds you issued, and pays out what is left, usually a few days later. So one payout line in the bank is:

If each order’s payment goes straight into your checking account in QuickBooks, the register shows 264.54 and 120.00 where the bank shows 337.79, and the reconcile window never comes out at zero.

The fix: payments wait, deposits match

QuickBooks Desktop already has the tool for this: Undeposited Funds.

1. Record each order’s payment into Undeposited Funds, not into checking. The invoice is paid; the money just hasn’t reached the bank yet.
2. Record each refund out of Undeposited Funds as well, so it can travel with the payout it was taken from.
3. When the payout arrives, open Banking > Make Deposits. Tick the payments that WooPayments included in that payout, and the refunds it took back.
4. Add the card fees as a line on the deposit, with a minus amount, to your merchant fees expense account.
5. Check the deposit total equals the bank line, then save it into your checking account.

Now the bank shows 337.79 and QuickBooks shows one deposit of 337.79. Reconciling is ticking one line.

Where to find what is in each payout

In WooCommerce, the WooPayments section lists each payout (deposit) with the transactions it contains: the charges, the fees and any refunds. Work from that list rather than from your order list, because a payout often includes orders from several days and leaves out others that are still on their way.

Two things that commonly trip people up:

• The fee is not on the invoice. If you take card fees off each invoice instead (so the invoice equals what you received), leave the fee line off the deposit; the payments already carry the net amount. Pick one method and keep to it.
• A payment deposited by itself. One payment put straight into checking will make that payout’s deposit short by exactly that amount. Move the payment back into Undeposited Funds (edit the payment’s Deposit To account) before making the deposit.

Doing it without the clicking

This is exactly what NemoWorks Sync does on its paid plans: payments and refunds wait in Undeposited Funds, and each WooPayments or Stripe payout becomes one deposit with its payments, fees and refunds, equal to the bank line. When the lines don’t add up to the payout, it stops and says why instead of guessing. The payout rules are in the help center.

More articles