QuickBooks Online automatically records fees deducted from your QuickBooks Payments transactions. Make sure your Payments account is set up so you can save time recording these fees.

Connect your QuickBooks Payments account to QuickBooks Online

  1. Select the Gear icon at the top, then Account and Settings (or Company Settings).
  2. Go to the Payments tab.
  3. If you already have an account, select Connect. If you don't have an account yet and want to sign up, select Learn More.

Once the accounts are connected, you'll be able to select the Expense account you want to use to track QuickBooks Payments fees.

Set an Expense account

  1. Connect your QuickBooks Payments account.
  2. Select the Gear icon at the top, then Account and Settings (or Company Settings).
  3. Go to the Payments tab.
  4. Select the Pencil icon.
  5. In the Chart of Accounts section, select the drop-down next to Where do you want to record processing fees?, then choose another Expense account.

    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.
    If you need to change the account, you have to access your QuickBooks Payments Account, which you can get to by selecting Manage account.

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.