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Hi mailserver09,
I also like the idea of assigning reference numbers to customers (students) to be used when they pay for a faster way to match transactions. However, this is currently not a feature in QBO.
By the way, bank transactions usually have the name of the payer/transferer, and I assume in your case that their amounts are equal to their invoices. Therefore, with payer and invoice amount details, they should detect their corresponding invoices as matches. Thus, you can simply accept the matched transactions in batches.
Another option is to create bank rules to automatically accept bank transactions as sales receipts. For example, if the bank transactions contain the name of the transferer/student in the bank details, you can set a rule that every transaction with their names will be automatically accepted as sales receipts in QBO. This is ideal if you're not doing invoices.
You can always go back to this thread if you have other questions about your bank transactions or student payments.