Woo Commerce Double Accounting Sales?

Thank you for choosing QuickBooks for your accounting needs, @SlabSentinel.

Usually, if you have connected your bank account and PayPal to QuickBooks, you can match your bank feeds directly to invoices that you created in QuickBooks. This way, it will prevent double accounting for your sales. When you haven't paired the received payments or created invoices in the system to your bank feed deposits, this is the reason it will double account sales.

When receiving payments, this will reduce the debtor's account normally while it increases your bank account. If you're receiving payments in QuickBooks and directly deposit them to your bank or PayPal account and at the same time have not matched them to payment record, this will create a duplicate revenue. You can consider excluding the bank transaction.

In addition, when your bank receives weekly deposits, those deposits can match multiple invoices. From your Banking window's For review tab, I suggest clicking the deposit transaction and then choose Find match. From there, you can either pick the invoices/payments manually or enable the Suggested Matches to select groups of QuickBooks income transactions. To learn more, check this article: Categorise and match online bank transactions in QuickBooks Online.

Alternatively, you can utilize the receive payment feature and deposit them into the Undeposited Funds (clearing account) account to hold funds and in QuickBooks, then link them by creating a bank deposit. This way, matching the weekly bank feed deposit transactions to QuickBooks deposits will be easy. Take a peek at this article: Deposit payments into the Undeposited Funds account in QuickBooks Online.

On the other hand, so when your WooCommerce already deducted their fees before depositing to your bank, these fees can be added as a category when you create a bank deposit in QuickBooks. Please make sure to put a negative sign on the amount to deduct the total value of the payment received so it will match the bank feed deposit. Take a look at the payment total below and how it works when adding those WooCommerce fees as a category:

Moreover, once you're all good, you can refer to this article on how to show your targets and sources to reflect efficiently on a report: Customise reports in QuickBooks Online.

To summarize everything, your bank transactions should match any transactions you created in QuickBooks. If you recognize that those bank feeds entries can't be found in the system, you can add or categorize them to show them in your bank register. So technically, when you record a Receive payment, QuickBooks will eventually match a bank transaction.

I'm still here, and please let me know if you have other banking concerns. I'll be around to help. Have a great day!

@SlabSentinel 

Consider having a 3rd party connector to reconcile your WooCommerce transactions and avoid duplication from payment processors.