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Record QuickBooks Payments deposits and fees in QuickBooks Online

by Intuit • Image Alt Text 57 •
Image Alt Text Updated 8/4/2026 00:15

QuickBooks Online automatically records deposits and fees deducted from your QuickBooks Payments transactions.

An icon showing cash and a payment card Check out QuickBooks Payments rates and apply. Then, you can automatically process payments, deposit funds and record transactions in your books.

Selecting your accounts

  1. Select the Settings icon ⚙, then Account and Settings.

  2. Go to the Payments tab.

  3. In the Chart of Accounts section, select the your accounts and save.

Note: Make sure the deposit account selected is the same account received payments get deposited to. It should also be the same account where fees are deducted from in real life.

About Batch Deposits

If you are using the Downloaded Transactions feature to connect to your bank, batches will automatically be matched. This is because your payments will automatically go into the Undeposited Funds account in QuickBooks Online as soon as you process them. Once they settle and are deposited into your checking account in real life, the Batch Deposit will automatically be recorded and a separate fee withdrawal will be automatically recorded in Fees withdrawal account.
QuickBooks Payments for OnlineQuickBooks Online AdvancedQuickBooks Online EssentialsQuickBooks Online PlusQuickBooks Online Simple StartIntuit Enterprise Suite

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