This is what you need to do!
First, when you create sales receipt or invoice > choose deposit to “Undeposited Funds” account, not bank account.
(I am giving lengthy steps, but it moves real fast)
Let us start from your banking center.
Find the deposit amount you want to match.
Highlight and click once. Transaction screen will expand.
Look for “Find Match” or “Find other match transactions.”
It will take you “Deposit” screen.
Select transactions to match (check customer payments). You are still looking at the gross level payments.
Getting closer, next step is where you make adjustments for Stripe fees.
Pull down “resolve difference” arrow and select “Add New Transaction.”
Select “Add New Transaction” and screen with expand with “Add New Transaction” section
You will also notice resolve difference amount which should be the same amount as Stripe Fees.
Go to “Add New Transaction” section
This is where you will enter Stripe fees.
Select account category (most likely merchant service fee expense account)
Enter negative amount for fees (same as resolve difference amount. example for ten bucks -10.00).
Save. Screen will disappear and it is posted to QuickBooks.
Back to banking center again!
If this does not work (because it was downloaded as bank transfer type), you will need to take manual route.
Bank Deposit (create + sign > other > bank deposit) > check payments > add fees to new transaction section as a negative amount. Same steps above.
Go back to banking center > now you should see green match sign > select match > done.
Click on the screenshots below to enlarge them