If I created an invoice with 2 line items, why did it automatically accept a partial payment when the invoice should have been paid in full?

I'm here to provide some details about invoice payments in QuickBooks, dwilliams-usphot.

In QuickBooks Online (QBO), you'll always have the option to make partial or full payments by entering the amount that you want to pay in the Payment column. The screenshot below shows an example of when a customer pays partial payment:

Aside from that, you'll have to record the payment in QuickBooks to mark the invoice as paid after you process a payment from a customer. If not, the invoice stays open and remains unpaid on your reports. You can record the full or partial payment on an invoice, and QuickBooks tracks any remaining balance.

To record payment for a single invoice

1. Select + New.
2. Select Receive payment.
3. From the Customer dropdown, select the name of the customer.
4. From the Payment method dropdown, select the payment method.
5. From the Deposit to dropdown, select the account you put the payment into.
6. In the Outstanding Transactions section, select the checkbox for the invoice you're recording the payment for.
7. Enter the Reference no. and Memo if needed.
8. Select Save and close.

To record partial payment for an invoice

1. Select + New.
2. Select Receive payment.
3. From the Customer dropdown, select the name of the customer.
4. From the Payment method dropdown, select the payment method.
5. From the Deposit to dropdown, select the account you put the payment into.
6. In the Amount received field, enter the amount your customer paid.
7. In the Outstanding Transactions section, select the checkbox for the invoice you're recording the payment for.
8. Enter the Reference no. and Memo if needed.
9. Select Save and close.

To see the remaining balance for the customer, you can follow the steps outlined below:

1. Go to Business overview and select Reports (Take me there), or go to Reports (Take me there).
2. Find and open the Customer Balance Summary report.
3. Select Run report.
4. Review the customer's open balance in the Total column.

Also, QuickBooks applies the payment to the invoice line items in order when you record partial payments.  Additional payments apply to the next line items until the payment is complete.

Additionally, you can put payments into the Undeposited Funds account until you're ready to combine them. For more information, you can check out this article for your guide: Deposit Payments Into The Undeposited Funds Account In QuickBooks Online.

Let me know if you have additional questions about accepting invoice payments. Please know the Community is always here 24/7 to assist your needs.