Subtract fee from manual QuickBooks Payments deposit

Forum|Forum|2 months ago
April 19, 2026
1 reply
42 views

Recently QuickBooks Payments decided to try to choke me out of business by withholding depositing payments until I verify some "account" information. The info: What services/products were rendered TO a vendor I made my first QuickBooks Bill Pay ACH transfer to. That idiocy is supposedly cleared up, and the withheld payment money "credited" (their word) to my bank, minus the fees which were taken out immediately.

So now I have a stack of CC payments that are not recorded as deposited, a lump deposit in the bank minus the CC fees for those payments, and a debit from the bank for the total of fees. So the big question:

How can I subtract the CC fee(s) from a manually created bank deposit of QuickBooks Payments payments?

QuickBooks Online

Best answer by Rusimyhr

Hi there, @CreativePrinters. I understand how challenging this situation with the delays and fees has been for your business. To make reconciling this lump sum easier, you can use the Bank Deposit feature. This tool allows you to bundle your individual payments into a single transaction that matches the exact net amount deposited by QuickBooks Payments.

To get started, go to + Create and select Bank Deposit, then check off all the relevant credit card payments. To adjust the total, go to the Add funds to this deposit section and add a line, selecting your bank fees or processing fees expense account. Once done, enter the fee amount as a negative number. For example, -15.00. This will change the deposit total to match the net amount received.

Regarding the separate fee debit appearing in your bank feed, please be cautious not to add it as a new expense, as this would double-count the fees you have already recorded in the deposit. Instead, categorize that bank feed transaction to the same fees expense account and ensure it reconciles against your bank statement. This keeps your books balanced and ensures your actual bank balance matches your QuickBooks records perfectly.

Please let me know in the comments if you have additional questions or concerns. We're here to help.

R

Rusimyhr

Answer

QuickBooks Team

Hi there, @CreativePrinters. I understand how challenging this situation with the delays and fees has been for your business. To make reconciling this lump sum easier, you can use the Bank Deposit feature. This tool allows you to bundle your individual payments into a single transaction that matches the exact net amount deposited by QuickBooks Payments.

To get started, go to + Create and select Bank Deposit, then check off all the relevant credit card payments. To adjust the total, go to the Add funds to this deposit section and add a line, selecting your bank fees or processing fees expense account. Once done, enter the fee amount as a negative number. For example, -15.00. This will change the deposit total to match the net amount received.

Regarding the separate fee debit appearing in your bank feed, please be cautious not to add it as a new expense, as this would double-count the fees you have already recorded in the deposit. Instead, categorize that bank feed transaction to the same fees expense account and ensure it reconciles against your bank statement. This keeps your books balanced and ensures your actual bank balance matches your QuickBooks records perfectly.

Please let me know in the comments if you have additional questions or concerns. We're here to help.

C

CreativePrintersAuthor

New Member

So far so good. It gets me the deposit I need and the payments out of limbo. It does add the fee amount as a deposit rather than expense to the account the fees are recorded to, which is only natural I would say.

If anything else pops up after the fact I'll let you know. Thanks.

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