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Record Merchant Service Deposits

Merchant Service Deposits tabs in QuickBooks Desktop

  • Add Online Payments - payments that could not be matched to an existing invoice in QuickBooks will show up here. Select Add Payment to record each payment. Optionally, you can create an invoice using the Need Invoice link. If you create an invoice here, you will need to apply the payment to the invoice by going to Customer > Receive Payments and apply the payment to the invoice.
  • Ready To Record - once all the transactions in a batch are matched and recorded, the batch will show up under Ready To Record and you can record the batch as a deposit. If all the transactions in a batch have not been recorded, you will not be able to record the batch and will get the message Transactions Not Added.
  • Recorded - view and monitor transactions that have been successfully recorded.
  • Errors - track transactions that need to be manually recorded in QuickBooks. If one or more transactions in a batch are in this tab, the batch will not be recorded. This is to ensure that the amount in QuickBooks matches the amount reflected on your bank statement.


If you are using QuickBooks for Mac

Merchant Service Deposits and Fees will need to be manually recorded as this feature is not available in QuickBooks for Mac.

To manually record transactions:

  1. In QuickBooks, go to Customers > Receive Payments and create an entry of the transaction.
  2. After receiving the payment, go to Banking > Make Deposits.
  3. Select all the payments in the batch and click Save & Close.

Record missing Deposits and Fees manually

Missing Deposit

  1. In QuickBooks, go to the Banking drop-down and select Make Deposits option (not make Merchant Service Deposits).
  2. Highlight the appropriate items to be reconciled.
  3. Click Make Deposits to move the items to the bank account and complete the reconciliation.

Missing Fee

To enter the missing fee, the corresponding bill will also need to be created.

Create the bill

  1. In QuickBooks, select Vendor > Enter Bill.
  2. At the Enter Bill window, select the vendor assigned for Intuit merchant service account (if not listed, select Add New).
  3. Ensure the proper expense account is listed in the Account field.
  4. Enter the amount of the fee to be entered in the Amount Due field (that value should also then appear in the amount filed below).
  5. Ensure the date is correct for the date of the fee then click Save & Close button to complete the bill.

Pay the Fee

  1. Go back to the Vendors drop-down and select Pay Bills.
  2. The bill that was just created will appear here. Place a checkmark next to the bill.
    Note: If there are multiple bank accounts, be sure to select the bank that the fees were withdrawn.
  3. Click Pay Selected Bills to complete the process. A confirmation window will appear.

Contact the QuickBooks Software Support team for additional assistance in making manual entries in QuickBooks.

Resolve Error: "In order to make a deposit, you need a valid expense account"

This error occurs due the insufficient user permissions in QuickBooks Desktop. All online payments are downloaded through Record Merchant Service Deposits. This is the window QuickBooks will try to open when clicking Get Online Payments.

To resolve this, the QuickBooks administrator needs to give the user’s role the following permissions:

  • Checks
    • Create
    • Print
  • Chart of Accounts
    • Create
    • Modify
    • View Account Balance

Configure deposit and fees account settings in QuickBooks

To download Merchant Service Deposits and Fees, an account will need to be chosen to download them into. Also, an expense account to assign the fees to and withdraw them from, will need to be chosen. This is typically the same bank account created in QuickBooks to reflect the actual bank account your funds are being deposited to and fees are being withdrawn from.

In the newer version of QuickBooks the deposit options can be seen by going to Record Merchant Service Deposits and then Change your deposit settings on the bottom left.

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