QB Issue Resolution:

The fastest way to match the payments is to use the Find Match option which is what you’re currently doing.

Time is really precious especially when doing business, and it would help you a lot if you can just select multiple payments per invoice. I’ll bring this idea to our product developers, and please do the same by sending them feedback through your QuickBooks account. You can click on the Gear icon and choose Feedback.

Resolution for Issue 'How do we match multiple payments over the course of a month to one invoice all at once? I get multiple payments per invoice each month and want to match them quickly!' available: Yes (Solved).
Source: Intuit Community forum.

How do we match multiple payments over the course of a month to one invoice all at once? I get multiple payments per invoice each month and want to match them quickly!: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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