How to Record Stripe Payments in QuickBooks

This article covers:

How Stripe deposits differ from client payments
How to record payments without errors
How to match the deposit in your bank feed

Why Stripe needs a special step in QuickBooks

Stripe collects funds from your client, deducts its fee, and then sends you one combined deposit. If you manually record this deposit to sales, you will duplicate the income that was recorded on the invoice.

Flow: Client pays → Stripe holds → Stripe keeps fee → Stripe sends deposit → Bank → QuickBooks

We need to adjust the client payment, subtracting the Stripe fee, then record the deposit to ensure QuickBooks matches the amount deposited by Stripe.

Step-by-Step Instructions to Record Stripe Payment

What happens when a client pays

Example:

Client pays: $1,325
Stripe deposits to your bank: $1,152.75
Stripe keeps: $172.25 (their fee)

All three numbers must be recorded correctly.

✔️Step 1 — Record the client’s payment

When the client pays:

The payment will be applied to their invoice in QuickBooks
The payrment should be recorded to Undeposited Funds (sometimes called Payments to Deposit)

Do not record the deposit directly into your bank account in QuickBooks. (See video)

✔️Step 2 — Create the Stripe deposit

When Stripe sends the money to your bank, you need to make the deposit in QuickBooks:

Go to "+ New → Bank Deposit"

Select the client’s payment (for example, $1,325)
Add Stripe’s fee as a negative line:
- Received From: Stripe
- Account: Merchant Fees
- Amount: the Stripe fee as a negative number (for example, -172.25)

Now the deposit total will equal the amount Stripe actually sent to your bank ($1,152.75).

Click Save & Close.

✔️Step 3 — Match it in Banking

Now, instead of categorizing the Stripe deposit, you only have to match the deposit to the one you just made.

Go to Banking → Transactions
Click Match next to the Stripe deposit.

Done.

⇒ Why this matters

This process:

Records your full client income
Tracks Stripe fees correctly
Prevents double-counting revenue

If you skip these steps, your books will show more income than you actually earned.

Common Mistakes

Recording the net deposit as full income
- Always record the full client payment first by applying it to the invoice in QuickBooks.
  Then record the Stripe deposit separately using a Bank Deposit, with the Stripe fee entered as a negative line. This keeps your income accurate and still matches your bank.
Skipping merchant fees
- When creating the Bank Deposit in QuickBooks, always add a second line. This ensures Stripe's cut is properly tracked as a business expense.
Not matching the bank transaction
- When recording client payments, always use Undeposited Funds (or Payments to Deposit) instead of your checking account.
- Then use + New → Bank Deposit to group those payments into one deposit that matches Stripe’s actual transfer.

Tips for Efficiency

Consider setting up Stripe as a vendor in QuickBooks to simplify fee tracking.
Use QuickBooks' built-in math function to calculate fees and net payments to avoid manual errors.
Regularly reconcile Stripe payments with bank deposits to maintain accurate financial records.