Deposited check on checking register but not appearing in customer/donor account.

Pleased to have you here, @Mrjan.

Welcome to the Community! I appreciate you for letting us know with what you did to resolve your concern on your end. Allow me to share additional information on how recording a deposit  works in QuickBooks Online.

In QuickBooks Online, you have two options to record a deposit :

• by creating a Sales Receipt 

• via the Bank Deposit 

If the transactions were downloaded from your connected bank account, it will stay on the For Review section in the Banking page.

To make sure this downloaded transactions are applied to your customer's account or existing manually created transactions, here's how:

1. Go to Banking.
2. Under Banking, choose For Review.
3. Locate the specific transactions.
4. Click the transaction to expand and see the rest of its details.
5. Click the Find Match or Add.
   • ​​​​​​​To Find Match
     1. ​​​​​​​​​​​​​​Click Find Match.
     2. In the Match Transactions page, use the filter options to locate the transaction that exactly match your bank deposit.
     3. Click Save.

         

   • To Add
     1. ​​​​​​​Click Add.
     2. Choose the Payee.
     3. Select the affected account.
     4. Choose the name of Customer.
     5. For the Class and Territory, it is optional.
     6. Type in the transactions description.
     7. Click Add.   

That should do it! You can always post in the Community page if you have other questions or want to share your best practices  in recording your transactions in QuickBooks Online. Have a great rest of your day.