When Jobber Payments sync over to Quickbooks, they sync over the full amount of the payment to the client as "Unapplied funds" or "Undeposited funds" and need to be reconciled to your correct Chart of Accounts within QuickBooks.
The amount deposited to the your bank account though is the total minus the processing fees. This is because Jobber Payments takes off the fee from each transaction before depositing it.
Reconciling deposits and payments to account for the Jobber Payments fees is done within QuickBooks. This is very similar to how you would handle processing fees for other credit card processors, such as PayPal.
When your bank account also syncs into QuickBooks, you’ll have two "unapplied" payments for the same Invoice. The payment note comes from Jobber and the deposit note comes from your bank account. The deposit note is the Jobber Payments transfer less the credit card fees. You will need to enter an adjustment for your credit card fees in the QuickBooks deposit section after matching up the deposit with the invoices from Jobber.
Jobber Payments Reports
You can find the total fees in two places: the Jobber Payments Transfers Report and the Transactions Report. You can find both of these reports by clicking the Reports tab from the sidebar.
The Jobber Payments Transfers Report will show each transfer of funds into your bank account. If you click into one of them, it will show the number of transactions, collected amount, net amount, and the fees. You can use the amount listed under fees as your adjustment in QuickBooks. This is probably the most straightforward way to see the total fees in a transfer.
Another way to calculate the fees for a transfer is by using the Jobber Payments Transaction Report. In this report you can see the exact amount of fees that were charged per transaction. You might need to click the "Columns" button to have it show the Fees column. Filter this report for the specific date range of all transactions that appear in the transfer to find the fees for that transfer.
We found this helpful article that is a good walk through for how to handle this in Quickbooks: https://5minutebookkeeping.com/how-to-enter-paypal-fees-and-merchant-fees-in-qbo/
If you need a refresher on the reconciliation process in QuickBooks Online, here is a tutorial that goes over this process: https://quickbooks.intuit.com/learn-support/en-us/bank-reconciliation/how-to-reconcile-an-account-statements-records-more/00/344822
We recommend consulting a certified accountant if you have any accounting questions about this.