QuickBooks Online enables a setting by default that we recommend each user disable. This is the "Automatically apply credits" setting in QuickBooks Online. When this setting is enabled, any pending payments, credits or prepayments get automatically applied to any invoice created for the same customer. We here at Bnbtally believe it is a mistake of QuickBooks to enable this setting by default, and many accountants disable it manually as it can cause issues for invoices. Here's how to disable it.
In QuickBooks Online, select the gear icon at the top right.
Select "Account and Settings"
Under "Automation" disable the option "Automatically apply credits"