Offset the payment of invoice against the loan

Welcome aboard to the Community, @DiaA1.

I can provide some information about how to handle a loan in QuickBooks Online.

Since it's a long term loan, you'll need to create a Long Term Liabilities account to record what you owe. Once done, If you plan to put your loan money directly into your bank account, we suggest creating a journal entry.

Here's how to create a liability account:

1. Click the Gear icon and select Chart of Accounts.
2. From the Account Type ▼ dropdown menu, select Long Term Liabilities. Note: If you plan to pay off the loan by the end of the current fiscal year, select Other Current Liabilities instead.
3. From the Detail Type ▼ dropdown, select Notes Payable.
4. Give the account a relevant name, like "Loan for a car".
5. Enter necessary information.
6. Hit Save and Close. 

To record the money you got from the loan:

1. Select + New.
2. Select Journal entry. Or, if you're in Business view, switch to Accountant view first. Then come back to these steps.
3. On the first line, select the liability account you just created from the Account dropdown. Enter the loan amount in the Credits column.
4. On the second line, select your bank account from the Account dropdown. Enter the same loan amount in the Debits column.
5. When you're done, select Save and close.

After following the steps above, you can now reduce the amount by recording a loan payment. Please follow these steps:

1. Select + New.
2. Select Check. Or if you're in Business view, follow the steps to switch to Accountant view first. Then come back to these steps.
3. Add a check number if you send an actual check. If you use direct withdrawal of EFT, enter Debit or EF in the Check # field.
4. Enter the following information in the Category Details section.
   1. First line: Liability account for the loan and the amount of payment.
   2. Second Line: Expense account for the interest and the amount.
   3. Additional lines: Any additional fees along with the appropriate accounts.
5. Select Save and close.

For the bank commissions charged, I suggest seeking expert advice from an accountant. This way, we'll be able to ensure your books are accurate and up to date.

Also, I've attached some articles you can use to records loans, as well as making payments:

• Set up a loan in QuickBooks Online
• How do I record the loan for an asset?
• Make a loan payment in QuickBooks Online​​​​​​​

Please know that the Community has your back if you need assistance. It’s a place for you to connect with experts and peers. Wishing you and your business continued success.