Showing results for 
Search instead for 
Did you mean: 
Everything you need to know about banking in QuickBooks Online - Discover more
Level 2

Woocommerce invoicing into Quickbooks

This maybe a very stupid question, but I can not find a very simple answer.

I have just started an ecommerce site as part of my main business. I have never got involved in ecommerce apart from eBay. Before going live with it, I have done some transactions to see how the payments from woocommerce work. 

I appreciate that woocommerce take a commission, but how are people entering it into Quickbooks?

For instance I sell a product for £10, generate the invoice etc, but get £9.50 from woocommerce. So my bank will never balance as the invoice is for £10 and not £9.50. 

Do you, wait until the woocommerce payment enters the bank, then generate an additional invoice to balance the bank? and the original sales invoice is not entered into Quickbooks?

I see there are "add on's" so woocommerce links with Quickbooks. Does this somehow, alter the invoice to amount received from woocommerce? I can not see how the bank transaction will ever balance. There are obviously thousands of businesses using woocommerce, but I can not find a simple explanation on how to account for the woocommerce payments.

QuickBooks Team

Woocommerce invoicing into Quickbooks

Hi there, @mrmunkeyman.


I'm here to help you match your bank statement and the invoice.


The difference in the amount is because of the bank fee. I'll walk you through to record fees. You can enter this as a new Service item or enter the bank fee amount into the register to match the bank statement. Then, enter the fee as a negative amount on the Bank Deposits screen upon depositing a payment.


Here's how:


  1. Click the Plus (+) icon, then click Receive Payments.
  2. Enter payment information and tick the check box next to the invoice where to apply for the payment.
  3. Choose Undeposited funds as the deposit to the account and click Save.
  4. Click the Plus (+) icon at the top and then click Bank Deposits.
  5. You should see the payment you entered in the Select Existing Payments section at the top.
  6. Place a checkmark to select the payment you want to deposit.
  7. From the Add other funds to this deposit section, enter the amount of the bank service fee charged to you by the credit card company as a negative amount.
  8. From the Account section, select the Expense account you usually use in tracking bank fees.
  9. Verify that the deposit amount is correct and click Save.

Once done, you can categorize and match your transactions. 


You can then reconcile your account to ensure your books are accurate with no duplicate transactions. You can refer to this article: Learn the reconcile workflow in QuickBooks.


Let me know if you have questions about managing transactions in QuickBooks Online. I'm always here to help. Have a great day.

Fiat Lux - ASIA
Level 15

Woocommerce invoicing into Quickbooks


You can use a 3rd party connector to reconcile WooCommerce transactions into QBO. 

Need to get in touch?

Contact us