If I have sent invoices and email confirmation saying they have been paid and quickbooks even reconciled on the system but no money is in the bank yet any ideas?

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If you’re new to QuickBooks Payments, your first deposit may take up to 5 business days because your account is still being set up. Once your account is fully established, deposits will speed right up.
 

To learn more about how timelines work, feel free to check out our guide: Find out when QuickBooks Payments deposits customer payments.
 

Let us know if you have further concerns.