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Yes, you can collect ACH payment from your customers in QuickBooks Self-Employed if the status of the application is Approved. It may take up to 3 business days to get the decision of the application, then you'll be notified thru your email.
However, if you haven't received an email within the time frame, I'd recommend contacting the Merchant Services Team to check your status of the application.
Here's an article for more information about recording payments in QuickBooks Self-Employed: Let your clients pay you online.
You can check this article for future reference to know more about ACH payments in QuickBooks Self-Employed: Add contractor direct deposit info in QuickBooks Self-Employed.
Fill me in if you have other concerns or questions by leaving a comment below. I'd love to help. Have a great day!