Yes, your customer can pay the invoice in two separate payments. When recording the payment transactions, input each amount under the Payment or Amount received section. Let me show you how:
From the Invoice page click on click on the Receive payment tab. Or, click Receive Payment from the (+) New icon.
Select the invoice from the Outstanding Transactions section.
Enter the first payment amount under the Payment column, then save the payment.
The invoice will now show it's current balance and the first payment made. Tap on Receive Payment to enter the second payment.
Choose a payment method, then enter the second payment amount.
Hit Save and close.
To learn more about recording invoice payment in QuickBooks Online, feel free to read the details from this article.
If you need additional resources managing your customers' transactions, you can also check out the topics from this link: Income and Expense help articles QBO.
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