Record Shopify Payouts and Fees in QuickBooks Automatically
Most Shopify to QuickBooks syncs record your sales but not the processing fees taken out of each Shopify Payments payout, so the deposit in your bank never matches the sales in your books. This workflow runs daily, finds each new paid payout, adds up the fees from its balance transactions, and creates a QuickBooks journal entry that splits the payout into the net deposit and the fee expense, so bank reconciliation lines up.
How it works
6 steps to make Shopify Payments deposits match QuickBooks without manual fee entries
Every morning
Every morning
Get yesterday's Shopify payouts
Get yesterday's Shopify payouts
Go through the payouts one at a time
Go through the payouts one at a time
Get the payout's transactions from Shopify
Get the payout's transactions from Shopify
Add up the payout's fees
Add up the payout's fees
Record a journal entry in QuickBooks
Record a journal entry in QuickBooks
Ready to make Shopify Payments deposits match QuickBooks without manual fee entries
Get setup in 6 minutes.
FAQs
Which accounts should I use?
That depends on how your sales are already recorded. The common setup posts sales to a Shopify clearing account, which this entry then empties. Confirm the accounts with your bookkeeper before turning it on.
Will this double-count if my sync app already records payouts?
Yes, it would. Check whether your sync app creates deposits first. If it records deposits but not fees, change the final step to record only the fee expense.
What about refunds and chargebacks?
They appear as balance transactions in the same payout, so the payout amount already reflects them. Add a separate line per transaction type if you want them broken out.
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make Shopify Payments deposits match QuickBooks without manual fee entries
6 min setup • Fully supported if you need help