Record Shopify Payouts and Fees in QuickBooks Automatically

6 min setup

No coding required

Runs 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.

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Schedule (Trigger)

Shopify Get List of Shopify Payment Payouts

Loop

Shopify Get List of Balance Transactions

Loop Sum

QuickBooks Create Journal Entry

How it works

6 steps to make Shopify Payments deposits match QuickBooks without manual fee entries

App connector: Schedule • Time to complete: 1 minute

Run once a day, for example at 8am.

App connector: Shopify • Time to complete: 1 minute

Get payouts with status paid dated yesterday.

App connector: Loop • Time to complete: 1 minute

Go through the payouts one at a time.

App connector: Shopify • Time to complete: 1 minute

Get the balance transactions for this payout by its payout ID. Each one carries its own fee.

App connector: Loop • Time to complete: 1 minute

Add up the fee field across the payout's balance transactions to get the total fees for this payout.

App connector: QuickBooks • Time to complete: 1 minute

Create a journal entry dated the payout date, with the payout ID in the memo: debit your bank account for the payout amount, debit a processing fees expense account for the fee total, and credit a Shopify clearing account for payout plus fees.

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Ready to make Shopify Payments deposits match QuickBooks without manual fee entries

Get setup in 6 minutes.

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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.

Personalize this template

Customize this workflow even further:

Attach the payout detail

Add a QuickBooks Upload Attachments step with a CSV of the payout's balance transactions, so the journal entry carries its own audit trail.

Post a Slack summary

Send the payout amount, fee total, and effective fee rate to Slack each day.

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make Shopify Payments deposits match QuickBooks without manual fee entries

6 min setup • Fully supported if you need help

Use this template →

Record Shopify Payouts and Fees in QuickBooks Automatically

How it works

Schedule (Trigger)

Shopify Get List of Shopify Payment Payouts

Loop

Shopify Get List of Balance Transactions

Loop Sum

QuickBooks Create Journal Entry

FAQs

Which accounts should I use?

Will this double-count if my sync app already records payouts?

What about refunds and chargebacks?

Personalize this template

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make Shopify Payments deposits match QuickBooks without manual fee entries