Why won't my QuickBooks Online deposit match my invoice when a payment processing fee changes the amount, and how do I fix it?

It's my pleasure. 

First, I'd like to ensure the attached payment is shown as deposited. You can do this by going to the + icon and selecting Bank Deposit. This is where you'll be able to locate the existing payment, select it using the box to its left, and then Save. 

Now that it's deposited, please go back to the Banking screen and see if you're able to match the payments. It's likely that QuickBooks will not find it for your because the amounts are different. If this is still the case, you have the ability to exclude the imported transaction. This can be done on the banking page by checking the box to the left of the transaction, clicking Batch Actions, and then choose Exclude Selected. 

I look forward to hearing how this goes for you. 

Thanks for joining this thread, @DebGer. I'm here to help you fix and match your old transactions without any further delay!
 

You have two options on how to handle merchant fees. You can use the Resolve Difference option to fix your payment difference. This helps match your transaction through its difference until it will be equal to zero. 
 

1. On the left pane, click Banking.
2. Select the For Review tab.
3. Choose the transactions to open.
4. Select the Find other records or Find match button to open the Match transactions window.
5. By default, the Match transactions window lists All transactions within the date range, but you can narrow the results.
6. Use options on the Show drop-down menu to specify the type of transaction you're looking for.
7. If the transaction you're looking for is outside the default date range, select the From and To date fields to change the dates.
8. If the amounts are different, you can locate additional matched transactions, or select Resolve Difference to open the Add resolving transaction fields to add the Category and Amount (and, optionally, Payee) of a resolving transaction until the difference equals zero.
   
9. If necessary, you can use the Add new transaction button to add multiple resolving transactions.
10. Click Save.
    
    

As another option, you can create a bank deposit for the merchant fee less than the amount of the invoice or sales receipt. This way, you can match this transaction to the downloaded bank transaction. You'll have to enter the merchant fee as a line item in the "Adds fund to this deposit" section. Then, select your new merchant fee expense account and enter a negative value that reflects the bank fee amount.  For more detailed instruction, go to the What about recording Bank Fees? section in this article: Bank Deposits.

 Once done, you can reconcile your account to make sure your books are accurate. Just go to the Accounting menu from the left pane and select Reconcile.

For more insights about this process, please refer to these articles:

• Add and Match Downloaded Banking Transactions
• Why Do I Occasionally Notice Penny Rounding Differences?
   

Drop me a comment below if you have any other questions.  I'll be happy to help you further. Have a great day.

Thanks ^ @Regina_Lend_A_Hand_Accounting!

@KaiBates, essentially, when you "make a deposit" with the transactions sitting in your Undeposited Funds, you can offset deposit and processing fees by adding individual transactions as lines item in the "Add funds to this deposit" section at the bottom. You can call them Bank Fees (I recommend including the name of the bank) or whatever you'd like, just make sure the fee goes into the same account as the associated transaction so the total (with the fee) now matches what's on your bank statement. 

If you need more step by step instructions, we wrote an article about making deposits. Hope this helps!