Connecting your Stripe account to Joy Pilot does two jobs at once:
Your customers can pay their invoices by card. Every invoice you send gets a secure Pay this invoice button, and the money goes straight into your own Stripe account.
Your Stripe activity flows into Joy Pilot like a bank feed. Payments, Stripe's fees and payouts to your bank all appear as transactions, ready to reconcile.
You only connect once — the same connection powers both.
⚠️ You'll need a Stripe account of your own. If you don't have one yet, you can create it during the steps below. Joy Pilot never holds your money: payments go directly to your Stripe account, and Joy Pilot takes no fee.
Step 1: Connecting your Stripe account
Go to the Bank Accounts section in Joy Pilot. You'll find it on your Dashboard home page, or on the Banking page.
Click
[ Connect a bank feed ]button.
Choose Stripe. You'll see a list of bank feed providers by region — Stripe is at the bottom, listed as Your Stripe account. Stripe isn't tied to a country, so it's available wherever you are.
Read the summary and click
Continue. This screen explains what's about to happen and what Joy Pilot will and won't do with the connection.Sign in to Stripe and approve the connection. Stripe will ask you to pick which of your accounts to connect, or to create a new one.
Stripe's approval wording is broad — it mentions seeing your account data and creating payments. That's Stripe's standard wording for this type of connection, and it covers exactly the two things described at the top of this guide: reading your transactions to build your bank feed, and creating a payment when one of your customers pays an invoice. Joy Pilot never moves money out of your Stripe account, never takes a share of your payments, and never issues refunds.
You'll be returned to Joy Pilot with your Stripe account connected.
💡 If you work with an accountant, note that the connection has to be made by you as the business owner — accountants can't connect a Stripe account on your behalf.
Step 2: Linking your Stripe feed to a bank account
Stripe holds a separate balance for each currency you trade in, so Joy Pilot creates one feed for each — for example Stripe (GBP). Each one needs linking to a bank account in Joy Pilot before transactions can come through.
Find your new Stripe feed in the Bank Accounts section.
Link it to a bank account. You can either create a new bank account for it (recommended — call it something like "Stripe") or link it to an existing one.
Import your transactions. The first import is done by you, so you can see what's coming in before anything is added to your books. After that, Joy Pilot imports new Stripe transactions automatically each day.
💡 Treat the Stripe feed exactly like a bank account, because that's what it behaves like: money arrives when customers pay you, Stripe deducts its fees, and payouts move the balance across to your real bank account.
Step 3: Sending an invoice your customer can pay
Once Stripe is connected, there's nothing extra to switch on. Any finalised, unpaid invoice can be paid by card.
Create and send your invoice as normal. In the send window you'll see a note confirming that a secure Stripe payment link will be included.
Your customer receives the invoice with a Pay this invoice button.
They can also pay from the invoice link. The web version of the invoice — the same link that's always been in your invoice emails — now shows the amount due and a Pay button.
They pay on Stripe's secure checkout page, which carries your business name, not Joy Pilot's. Stripe emails them a receipt automatically.
What happens after your customer pays
This is the part worth understanding, because it's slightly different from what you might expect.
The invoice doesn't mark itself as paid straight away. Instead:
The payment appears on your Stripe bank feed, usually within a few minutes.
You reconcile it against the invoice, the same way you'd reconcile any other payment.
That reconciliation is what marks the invoice as paid and records it in your books.
In the meantime, Joy Pilot shows you what's happened. On your sales list the invoice gets a purple tick, and opening the invoice shows a note reading "Paid by card via Stripe." Your customer sees a "Payment received — thank you" message on the invoice page.
This keeps your books accurate: nothing is recorded as received until the money is genuinely in your Stripe account and you've confirmed the match.
Reconciling a Stripe payment
When you open your Stripe feed on the Bank Reconciliation page, a single customer payment appears as two lines:
Line | What it is | What to do with it |
+ £120.00 — "Invoice INV-0042" | The full amount your customer paid | Reconcile it against the invoice |
− £2.45 — "Stripe fees: Invoice INV-0042" | Stripe's processing fee | Reconcile it to an expense account, such as bank or payment charges |
Splitting the payment this way means the invoice reconciles for the exact amount on it, and Stripe's fee is recorded as the business expense it is.
When Stripe later pays out to your real bank account, you'll see a third line — a payout — on the Stripe feed, and a matching deposit on your normal bank feed. Reconcile those two against each other as a transfer between accounts.
Stripe's fees
Joy Pilot doesn't charge anything for this and takes no share of your payments. You pay Stripe's standard processing fees, which are deducted before the money reaches your balance and appear on your feed as their own line. Stripe's current rates are on stripe.com/pricing.
Disconnecting Stripe
You can disconnect at any time, from either end:
In Joy Pilot — open the Stripe feed from the Bank Accounts section and choose to unlink it.
In Stripe — go to Settings → Authorised applications and remove Joy Pilot.
Disconnecting stops new transactions importing and removes the Pay button from your invoices. Transactions already imported stay in your books, exactly as they should.
Common questions
Do I need a Stripe account before I start?
No — you can create one during Step 1. You'll need to complete Stripe's own identity checks before you can take payments, which Stripe handles directly with you.
Does the money go through Joy Pilot?
No. Payments go straight into your own Stripe account. Joy Pilot never holds your money.
Why does my invoice still say unpaid after my customer paid?
That's expected — see What happens after your customer pays above. The invoice is marked paid when you reconcile the payment on your Stripe feed.
Can my customer pay part of an invoice?
Not at the moment. The Pay button charges the full outstanding amount.
I already use Stripe for other things — will those transactions appear too?
Yes. The feed brings in all activity on the connected Stripe account, not just payments for Joy Pilot invoices, so your Joy Pilot balance matches your real Stripe balance.
My Stripe account isn't in the list when I try to connect.
Stripe won't let an account be connected if it's already controlled by another platform — for example, if it was created for you by an online shop provider. You'll see it listed as ineligible. In that case you'll need to connect a Stripe account that you own directly.
Can I still get paid by bank transfer?
Yes. Your bank details still appear on the invoice as usual — the Pay button is an extra option, not a replacement.