Connecting Stripe to Mercury Books brings your sales, refunds, processing fees, and payouts into your books automatically, so you don't have to enter them by hand or work backward from your bank deposits. This article explains what comes in, how it posts, and how to sort out the most common issues.
Connecting Stripe
- Go to Accounts in Books
- Click Link account > Payroll or payment processor and select Stripe
- Authorize Mercury to read your Stripe data
- Map your ledgers — pick or create a revenue account, a fee account, and a refund account
- Set the date you want Books to start pulling Stripe activity from
Books also creates an account in your chart of accounts representing your Stripe balance. Sales and fees post there until the money is paid out to your bank.
Note: Nothing syncs until the ledger mapping step is complete. If you connected Stripe and your books are still empty, this is almost always why.
What comes in
- Charges — your sales, posted as revenue
- Refunds — posted to your refund account
- Processing fees — posted to your fee account
- Taxes collected through Stripe
- Payouts — the transfers from your Stripe balance to your bank account
The connection is read-only. Books reads from Stripe and never writes back.
How it posts to your books
Stripe activity doesn't post to your bank account — it posts to your Stripe account in Books, which works like a clearing account:
- A customer pays you. The gross sale posts as revenue, the processing fee posts as an expense, and the net sits in your Stripe balance
- Stripe pays out to your bank. The payout leaves your Stripe balance and the deposit arrives in your bank feed
- Books recognizes the two sides as the same money and links them as a transfer between accounts, so the deposit isn't counted as additional revenue
This is why your Stripe revenue and your bank deposits won't match line for line — the deposit is a transfer, not income.
Tip: A payout deposit can be categorized as revenue for a short time before Books receives the payout event and links it. If a deposit looks miscategorized, check it again the next day before you change it by hand.
Reconciling Stripe
Your Stripe account in Books reconciles like any other account, on monthly windows. Reconcile it against your Stripe balance for the period.
Your bank account reconciles against your bank statement, where payouts appear as deposits linked to your Stripe activity.
See our Reconciling accounts in Mercury Books article.
Matching Stripe payments to invoices
If you invoice customers who pay through Stripe, you can match the payment to the invoice so your accounts receivable clears. Open the transaction, choose to match the payment, and select the invoice — Books suggests a likely match automatically.
See our Matching payments to invoices, bills, and payroll article.
Troubleshooting
Stripe is connected but nothing is syncing.
The ledger mapping step isn't finished. Go to Accounts, open your Stripe row, and complete it.
I don't see the Stripe integration I set up.
Stripe appears in a few places across Mercury — a Stripe connection used for accepting card payments on Mercury invoices is separate from the Books integration. Connect Stripe from Accounts > Add account in Books.
Older payouts aren't linked to their deposits.
Payout linking applies to payouts that arrive after your connection is set up. For earlier ones, categorize the deposit as a transfer between accounts yourself.
My revenue looks too high.
If you were categorizing Stripe deposits as income before you connected Stripe, those deposits and your new Stripe sales both count. Recategorize the earlier deposits as transfers between accounts.
FAQs
Does Books pull my Stripe subscriptions?
No. Books reads Stripe transactions rather than subscription records, so there's no revenue recognition schedule from Stripe billing.
Does Books support Stripe Connect or Express accounts?
Not currently. Only your own Stripe account's activity is brought in.
Will connecting Stripe change anything in Stripe?
No. The connection is read-only.
Can I change which accounts Stripe posts to?
Yes. Open your Stripe connection from the Accounts page and update the ledger mapping.
Mercury is a fintech company, not an FDIC-insured bank. Banking services provided through Choice Financial Group and Column N.A., Members FDIC.