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How to enter an invoice which has already been paid?

If you are viewing this answer then most likely you want to enter already paid bill into QuickBooks then you have to enter them into QuickBooks and track the bills which have already paid in the past by using Bill Pay.

Enter a Bill which has already Been Paid to QuickBooks

We can see this by this example

We have 
been given a grant for free food, brush and toys for dogs in our city. Last week, we received our bill from the clinic. Since we paid the bill by check since it is displayed on the bills and then recorded it under our QuickBooks bills. Now the bill appears as paid.

New invoice 
has all of the current fees plus the $5.00 you owe. How do you address the error plus the additional charges? You must include the correction so that you are able to trace the Item when preparing reports on the grant.