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Level 2

Record net negative Stripe deposit when refunds exceed payments?

We have a low volume Shopify store using the Stripe payment gateway. We process store orders (monthly) in QB Desktop as follows:

  1. create invoice(s)
  2. receive payments on “Visa” leaving the box to process payments unchecked
  3. record deposit, adding a line to reduce deposit amount by Stripe Fees (an expense account)

This month, a paid but unshipped large order from several months ago was refunded from within Shopify/Stripe, and another unrelated small order was received. For example:

  • REFUND: -100.00
  • NEW ORDER: 50.00
  • NEW FEE: -1.00
  • NET RESULT: -48.00 (pulled from checking acct)

We entered the new order invoice as normal, then created a Credit Memo for the refunded order, and chose to refund to back to “Visa”, and left the process payments box unchecked. However this makes the total to deposit a negative, which cannot be saved in QB.


Question 1 – should we have wrote a check instead, for $100 minus the $3 adjustment, then entered a deposit for the new order only?

Question 2 – if writing a check for refund, is it appropriate to use the Stripe Fees account, for $97 out to customer?

Question 3 – unsure how to remove the unprocessed Visa refund. Will voiding the CM clear it out?



2 Comments 2
Level 2

Record net negative Stripe deposit when refunds exceed payments?

Update: I was able to find and delete the Visa refund from the Accounts Receivable register. Then I refunded via check (not printed), and decided to handle this situation with two separate entries that we'll add together at time of reconciling the bank account. One being the refund amount (-100), the other being a deposit of new order, new order fee, and refund adjustment (52).

QuickBooks Team

Record net negative Stripe deposit when refunds exceed payments?


Hey there, sevans.


Thanks for being part of the QuickBooks family.  I’m happy to know you’re able to fix the negative deposit showing in your Stripe account.

The steps you’ve taken will help customers who are having the same problem when recording refunds from Shopify to Stripe. Aside from posting questions, the Community platform is a great platform to share your thoughts, ideas, and best practices using QBO.

For future reference, check out this article with detailed instructions on how to record a refund: Credit memo or refund in QuickBooks Desktop.

That should get you in the right track.

Reach out to me if you have additional questions about the product. Please know I’m just a comment away for help. Have a good one.


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