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Credit a credit note for your customer to apply to a future invoice. These can be created if your customer overpaid, or as a referral system. 

Create a Credit Note 

Sales > Credits > +New Credit Note

Select a Customer for whom Invoice has been made and you want to apply Credits to. Fill in all other required details. Click Preview or Save as Draft.

Note: Grand total should be lesser or equal to the Invoice Balance Due/Grand Total to applying for this Credit.

Click Send Credit Note.

To Apply a Credit Note

Go to the Invoice Preview against which you have to apply for this Credit. Click Apply Credit.

Apply Credit pop up appears where select a Credit Note from the dropdown which you want to apply for payment. Also, fill in other required details. Click Apply Credit.

This is how Credit Note is applied and payment is made against Invoice:

Notes:

1. Once Credit Note is applied, Credit Note status automatically changes to Closed.

2. You can also revert this payment by simply clicking the Delete icon shown in the above screenshot.

3. Once it is reverted, the status of Credit Note changes to Open automatically and you can again apply it against any Invoice for the same Customer.

Here is a video showing how to do this.