The deposit of your customer's payment takes time for it to show on the system. The deposit speed depends on the product you're using and the type of payment.
For credit card payment, deposits take one to two business days. As for bank transfer (ACH) payment, it will take two to seven business days. You can review the deposit status either on your QuickBooks Online account or through the Merchant Service Center, it depends on where you process payments.
Also, to ensure your accounts match your bank and credit card statements, you can reconcile the transactions. Here's an article as your guide: Review your accounts.
Know that you can always get back to the Community if you have any other concerns. I'll be right here to help. Take care!