I have a transaction that's come through after I've created the invoice. How do I now link the payment to the invoice so it shows a paid by the customer?

Hi there, @ajtilds-gmail-co. I'm here to provide you with steps in linking payment to an invoice.

If it is a payment registered through bank deposit, below are the steps you can perform to link it to the invoice. Let's start with editing the deposit.

1. Go to the Gear icon and choose Chart of Accounts.
2. Look for the account you deposited the payment to and click View register.
3. Locate and select the correct deposit and then select Edit.
4. From the Add funds to this deposit field, mark the deposit.
5. Next, select the Received From dropdown and choose the customer the deposit was from.
6. Click the Account dropdown and pick Accounts Receivable.
7. When done, select Save and Close.

Once finished, let's now apply the deposit as an invoice payment:

1. Navigate to the + New button.
2. Then, choose Receive Payment.
3. Pick the Customer from the dropdown. You'll see all open invoices and outstanding credits for that customer.
4. Enter the day you received the payment, in the Payment date field.
5. From the Outstanding Transactions section, check the invoice you need to mark as paid.
6. Under Credits, click the deposit.
7. When done, select Save and Close.

For your reference about the process, feel free to check this article: How to link a bank deposit to an invoice. 

I've also added this helpful link that will serve as your guide in managing invoice payments: Record invoice payments in QuickBooks Online. It also includes steps on how you can enter a partial payment and utilize the Undeposited Funds account. 

You may also want to print or send payment receipts to your customers so they have a reference on their transactions. To do so, refer to these steps:

1. Go to the Sales menu and choose Customers.
2. Look for the customer you recently recorded a payment with. Click the name to open.
3. Under the Transaction List tab, find the payment transaction and click it to open.
4. Select the Print option at the bottom part of the page if you want to print the receipt.
5. Choose Save and send button if you want to send the receipt to your customer.

Don't hesitate to get back here if there's anything else you need about linking payment to an invoice. I'd be glad to know your results. Have a good one.