Bulk processing sales receipts?

Hi, I have a client that processes monthly subscription fees.  We have just taken over the bookkeeping for this client.  The sales invoices are all set up for recurring transactions that are processed automatically each month.  However, the payment of these invoices has been handled manually by processing a sales receipt to each invoice per the bank statement when it is received. 

The previous bookkeeper had bank feeds setup but said that the QBO transactions it was selecting were never correct and it got very messy.  Most of these payments are paid by direct debit each month that have been set up by our staff. (therefore we can edit the descriptions)  Some of the payments are made externally by the clients themselves.  

What would you suggest is the most efficient way of processing these transactions?  There are currently around 1000 to process each month.  Is there an app that can assist if QBO can't do this efficiently itself?  




There may be a 3rd party app, but if you have a merchant account through QuickBooks Online, you can just setup recurring Sales Receipts instead of Recurring Invoices.  That way it creates the sale transaction, emails a receipt to the customer, and processed the payment all in 1 shot.  No need to enter a 2nd transaction for receiving the payment for each monthly charge from a customer.

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