Marking a Stripe Invoice Paid Outside Stripe in QuickBooks

A customer gets your Stripe invoice, ignores the payment link, and mails a check. You deposit the check at the bank, open Stripe, and mark the invoice paid so it stops chasing them. Perfectly reasonable.

Now QuickBooks has a problem. There is an open invoice sitting in Accounts Receivable, cash that arrived in your operating account, and no Stripe charge connecting the two. The account you normally use to reconcile Stripe will not help you here, because the money never went through Stripe at all.

This post covers exactly what Stripe does when you mark an invoice paid outside Stripe, what that leaves behind for QuickBooks, and the one Acodei setting that decides whether the resulting payment lands somewhere you can actually reconcile.

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What "paid out of band" means in Stripe

Stripe's name for this state is paid out of band. There are two ways to get there:

• Dashboard: open the invoice, click More, choose Change invoice status, then select Paid.
• API: call the Pay Invoice endpoint with paid_out_of_band: true.

Stripe documents that parameter as: "Boolean representing whether an invoice is paid outside of Stripe. This will result in no charge being made. Defaults to false."

Read that second sentence again, because it is the whole story. The invoice flips to paid and Stripe stops sending reminders, but Stripe never creates a charge. No payment method is touched, no processing fee is assessed, and no money enters your Stripe balance.

Stripe also warns that the change is one way: "This action is final, and the invoice cannot be altered after being marked as paid out of band." If you mark the wrong invoice, you cannot walk it back. That matters more than it sounds, and we will come back to it.

No charge means no balance transaction

A balance transaction is Stripe's record of money moving through your Stripe balance. Every successful charge creates one, carrying the gross amount, the fee, and the net. Your payouts are built from them: a payout is a batch of balance transactions moving from your Stripe balance to your bank.

An invoice paid out of band creates none of these. The consequences follow in a straight line:

• The money is not in your Stripe balance, because it never got there.
• It will never appear in a Stripe payout.
• It will never show up in Stripe payout reconciliation, no matter how far back you look.

The cash came in through a completely separate path: a check, a wire, or an ACH transfer straight into your bank account. Acodei's own documentation makes the same point about this scenario. When you mark an invoice paid outside of Stripe, an invoice payment entry can still be created in QuickBooks, but it will not show as a Stripe balance transaction.

This is where books go wrong. If that QuickBooks payment gets booked to your Stripe clearing account, the clearing balance goes up by an amount that no future payout will ever bring back down. The account is supposed to return to zero once each payout lands. Instead it drifts up by the value of every out-of-band invoice, and at month end someone spends an hour hunting a variance that was baked in weeks earlier.

What Acodei does with an out-of-band invoice

With Invoice Sync enabled, Acodei mirrors your Stripe invoices into QuickBooks Online. When a Stripe invoice is finalized, Acodei creates a QuickBooks Invoice reproducing the line items and tax lines allowed by your mapping settings. When the invoice is paid, Acodei creates a Payment (or a Credit Memo, for credit balance offsets) and applies it to the invoice it created earlier. Where that payment is placed depends on your holding account setting, Undeposited Funds or a non-Undeposited-Funds clearing account. Invoice Sync is a paid plan feature, toggled per company under Account Mapping > Premium Features.

Out-of-band payments have their own switch: Payments Marked as Paid Outside Stripe. It is off by default. Turned on, it generates a payment in QuickBooks when you mark an invoice paid manually in Stripe, and it can route that payment to Undeposited Funds regardless of your normal holding account.

That routing override is the important half of the setting, because it is what keeps the reconciliation problem above from happening. Undeposited Funds is a holding spot for money you have received but not yet matched to a bank deposit. That is precisely the state a mailed check is in. The payment waits in Undeposited Funds until you record the real bank deposit, you match them, and the money lands in the operating account where it actually arrived. Your Stripe clearing account is never touched, so it keeps reconciling against Stripe payouts the way it should.

Three setups that work

1. Leave the setting off and record the payment yourself. Acodei still syncs the invoice, so Accounts Receivable is correct. When the check clears, you record a Receive Payment against that invoice in QuickBooks and deposit it like any other check. This is the least automated option and the most obvious to an accountant reading the books later. If out-of-band payments happen twice a year, stop here.

2. Turn the setting on and route to Undeposited Funds. Acodei creates the payment against the right invoice when you mark it paid in Stripe, and parks it in Undeposited Funds. Your job shrinks to matching it against the bank deposit. This is the right answer if you invoice through Stripe but regularly get paid by check or wire, which is common for larger B2B invoices where the customer's AP department will not use a payment link.

3. Stop using paid out of band. Acodei's documented best practice is to avoid marking invoices paid outside Stripe unless it is truly necessary, and to prefer real Stripe charge events instead. If your customer sends a wire but you can plausibly collect through Stripe next time, collecting in Stripe keeps one system as the source of truth for both the receivable and the cash.

A worked example

You invoice a client $4,800 through Stripe. They mail a check.

In Stripe: you mark the invoice paid out of band. Invoice status becomes paid. Balance transactions created: zero. Stripe fees charged: zero, since there was no charge to process. Your Stripe balance is unchanged, and the next payout is unaffected.

In your bank: $4,800 arrives as a check deposit, on whatever day you got to the bank.

In QuickBooks with the setting on: the $4,800 invoice is already there from Invoice Sync. A $4,800 payment is created against it and sits in Undeposited Funds. Accounts Receivable drops by $4,800 and the invoice shows as paid.

Your one manual step: record the bank deposit and include the Undeposited Funds payment, so the deposit matches the $4,800 on the bank statement. Undeposited Funds returns to zero for that item.

Notice what is not in this flow. No Stripe fee expense, because Stripe charged none. No payout line. No entry in the Stripe clearing account. The only two accounts that move are Accounts Receivable and your bank.

Details that trip people up

QuickBooks Automatic Application has to be on. Acodei relies on it so payments and credit memos settle invoices automatically. With it off, you get a payment and an invoice that never link, and Accounts Receivable stays overstated even though the payment exists.

The Stripe side is irreversible. Marking the wrong invoice paid out of band cannot be undone in Stripe. In QuickBooks you can delete the resulting payment, but Stripe's invoice stays paid forever, so the two systems disagree from then on. Slow down on the confirmation dialog.

Invoice numbers get a suffix. Acodei appends -AC1, -AC2, and so on to synced invoice numbers by default, which prevents duplicate number errors when someone also hand-enters invoices in QuickBooks. When you go looking for the out-of-band invoice, search the customer and amount rather than the bare Stripe number.

Stripe fees never ride on the invoice. Acodei never adds Stripe fees to a synced invoice, because doing so would make the QuickBooks total disagree with the Stripe total. Fees are handled through sales receipts, deposits, or expenses under your fee management rules. For an out-of-band invoice this is academic, since there is no fee, but it explains why the invoice total is clean.

Amount validation depends on your tax setup. Acodei compares the finished QuickBooks invoice against the Stripe invoice amount to catch mismatches, and that exact-amount comparison applies when tax is enabled. If your totals look off, the invoice mismatch guide walks through the usual causes.

Partial credits are a different mechanism. If part of the invoice was written off with a Stripe credit note before the check arrived, that piece becomes a QuickBooks Credit Memo, not a payment, and it reduces the invoice without any cash moving.

Fix problems by resyncing, not by hand editing. Acodei's guidance for accounting teams is to resync from the Data Feed instead of manually altering the synced transactions in QuickBooks. A resync rebuilds the records from the source data, which keeps the entry explainable later.

FAQ

Does marking a Stripe invoice paid out of band charge my customer? No. Stripe documents paid_out_of_band as resulting in no charge being made. The invoice is marked paid, no payment method is touched, and no Stripe fee is assessed.

Will the money show up in my Stripe payout? No. Without a charge there is no balance transaction, and payouts are built entirely from balance transactions. The cash reaches you through whatever channel the customer actually used, usually a check or wire straight to your bank.

Why does Acodei route these payments to Undeposited Funds? Because the deposit is a real bank deposit and not a Stripe payout. The Payments Marked as Paid Outside Stripe setting can route the payment to Undeposited Funds regardless of your normal holding account, which keeps it out of the Stripe clearing account and lets you match it against the actual bank activity.

Can I undo an invoice marked paid outside Stripe? Not in Stripe. Stripe states the action is final and the invoice cannot be altered afterward. You can correct the QuickBooks side, but the two systems will disagree about that invoice permanently.

Should I turn the setting on? Turn it on if customers regularly pay Stripe invoices by check or wire. Leave it off if it happens rarely and you would rather record those few payments by hand. Either way, Acodei's documented preference is to collect through Stripe when you reasonably can, so the receivable and the cash live in one place.

Where this leaves your books

An invoice paid outside Stripe is a normal business event with an awkward accounting shape: the receivable lives in Stripe, the cash lives in your bank, and nothing connects them inside Stripe. Getting it right is mostly about sending the payment to the correct holding account, so your Stripe clearing account keeps meaning what it is supposed to mean.

Acodei syncs the invoice, creates the payment against it, and can put that payment in Undeposited Funds where a check deposit belongs. Start a free trial to see how your Stripe invoices land in QuickBooks, or compare plans first.