Hello there, @Elysha.

I understand that the deposit contains the net amount from invoice less fees. When you receive payment, it should be the gross amount to match it seamlessly. Worry less, I can help you record it in QuickBooks Desktop (QBDT).

In QBDT, we have two ways to record these charges into the program. First, delete the existing deposits and redo the recording process to include them. To proceed, follow the steps below:
 

1. Go to the Accountant menu and select Chart of Accounts.
2. Locate the Bank account and find the deposits.
3. On the deposit page, you can click Edit, then delete, or hold Ctrl + D.
    

Next, recreate the deposit, check out this article for guidance: Record and make bank deposits in QuickBooks Desktop.

Second, you can edit the deposit to add another line item. Let's begin by making a service item on the Lists and assigning an Expense account.

Here's how:
 

1. Go to Lists, then select Item List.
2. Select Item then New, then select New Item.
3. Choose Other Charge as the type of item you want to create.
4. Enter the Item Name/Number.
5. From the Account area, you ca select Other Expenses or any expense account. If you're not sure what to choose, consult with your accountant.
6. Fill in all the necessary information.
7. Then, hit Save.
    

Once done, return to the deposit and add the newly created Bank fees item in a negative amount. This will automatically subtract from the invoice payment while tracking the charges in QuickBooks.

If you want to combine payments into a single record, you can refer to this article for reference: Deposit payments into the Undeposited Funds account in QuickBooks Desktop.

Furthermore, I'm leaving these helpful guides in managing your bank transactions and reconciling accounts to always match your statements:
 

• Add and match Bank Feed transactions in QuickBooks Desktop
• Reconcile an account in QuickBooks Desktop
   

In case you have clarification with recording the invoice payments with a fee deduction from the collection agency, add them in the comments below. I'll be here to answer them for you.

Thank you @GebelAlainaM.

I had not deposited the check. I have everything set up already. 

Can you please elaborate on this section of your message:

"Once done, return to the deposit and add the newly created Bank fees item in a negative amount. This will automatically subtract from the invoice payment while tracking the charges in QuickBooks."

Thank you.

Thanks for checking back with us, @Elysha.

Since you haven't deposited the check, you can also try the steps that some of our other users have found successful when entering a payment from a collection agency. 

First, you'll need to create a wash account to move the money from one account to another when you cannot do it directly.

Once done, you can create a journal entry to transfer the amount from the collection agency to the clearing account. Here's how:

1. Go to the Company tab.
2. Choose Make General Journal Entries.
3. On the first line, debit the Accounts Receivable with the amount to be transferred then add the customer name in the Name column.
4. On the next line, credit the Clearing Account.
5. Click Save & Close.

After that, you can now link the payment to the journal entry. To do this:

1. Go to the Customer tab.
2. Select Customer Center.
3. Choose the customer from which you're transferring the payment, then go to the Transactions tab.
4. Double-click the payment and mark the journal entry.
5. Click Save & Close.

Now, you'll need to create another journal entry to move the payment from the clearing account to the customer. Here's how:

1. Go to the Company tab then choose Make General Journal Entries.
2. Credit Accounts Receivable with the amount to be transferred then select the customer name in the Name column.
3. Debit the Clearing Account.
4. Click Save & Close.

Lastly, you can now apply the credit to the unpaid invoice. Here's how:

1. Go to the Customers tab.
2. Choose Receive Payments.
3. Select the customer you're transferring the payment to.
4. Mark the appropriate invoice and select Discounts & Credits.
5. Go to the Credits tab and select the credits you want to apply.
6. Click Done.
7. Click Save & Close.

That should do the trick. Keep in mind it's always best to consult with your accounting professional before making any changes to your company file. If you don't have an accountant, don't sweat it. You can find one here in our Resource Center. 

Please don't hesitate to let me know if you have any additional questions or concerns about this process. Take care! 

Thank you @Tori B ,

I still have the amount paid to the Collections agency listed in the Active Customers as to be paid by the customer. The fee paid did not go to "Collections".

I appreciate you getting back to us here in the thread, Elysha.

One of the possible causes why the paid amount didn't go to collections is that you may have to record the transactions differently.

With this, let's review the accounts and the journal entries you've previously made in your QuickBooks Desktop (QBDT) account.

Lastly, if there are any discrepancies in the accounts used and you're unsure how to proceed, I'd suggest consulting your accountant for proper handling. If you don't have one, you can use our Find-an-Accountant tool to look for an expert near you.

For future reference, you can always check out this helpful resource for you to be able to take action and minimize delayed collection of dues: Show Past Due stamp on invoices in QuickBooks Desktop.

I'll always be around any time you require additional assistance managing invoices in your QuickBooks Desktop account. Let me know in this thread so I can further back you up.