How do I close off an invoice that has only been partially paid and will not be fully paid? Will this impact GST reporting due to using the accrual system?

Hello, @kristy66.

You can record an invoice as a bad debt and write it off when it becomes uncollectible. By doing this, the customer's outstanding balance is removed, your expenses are correctly updated, and any GST liability related to the sale is adjusted.

There are two ways to record bad debt in QuickBooks Online.

• Direct Method
  1. Create a bad debt expense account. 
  2. Create a bad debt item. 
  3. Create an adjustment note for the bad debt. 
  4. Apply the adjustment note to the invoice.
• Allowance Method
  1. Create a bad debt expense account. 
  2. Create an allowance for bad debt account. 
  3. Create a bad debt item. 
  4. Create an adjustment note for your invoice. 
  5. Apply the adjustment note to the invoice. 
  6. Enter a journal entry for the allowance account. 

You can check this article for more detailed instructions: Write off bad debt in QuickBooks Online.

Meanwhile, the bad debt may affect your GST reporting depending on whether you're on a cash or accrual basis. Since you're using accrual-based, writing off a bad debt will only affect your GST if it has already been reported and paid. 

I'd recommend consulting with an accountant so you'll be guided accurately in tracking your unpaid invoices.

Let me know if you have other questions. I'm always here to help.