Knowledge Base Getting Started Frequently Asked Questions

How to take invoice payments with Stripe

This article explains how to start accepting debit and credit card payments for your FreeAgent invoices using Stripe.

Stripe lets your customers pay you by debit or credit card. Stripe charges you:

  • 1.4% + 20p for European-issued cards (Visa, Mastercard and American Express)
  • 2.9% + 20p for non European-issued cards

You can also collect invoice payments online using PayPal and GoCardless.

Setting up Stripe in your FreeAgent Account

1. Enable Stripe

Navigate to the drop-down menu in the top-right corner of the screen and select 'Connections'. 


Select 'Manage Stripe'.


Select 'Connect with Stripe'.


2. Sign in to Stripe or create your Stripe Account

If you’ve never used Stripe before, enter your email address, select ‘Next’ and follow the on-screen instructions to create a new Stripe account. If you already have a Stripe account you'd like to use, enter the email address associated with that Stripe account and select ‘Next’ to connect your Stripe account to FreeAgent.


Once you've created a Stripe account, or signed in to Stripe, you'll be taken back to the Stripe screen in FreeAgent.

If you ever want to disable Stripe in your FreeAgent account, navigate to ‘Settings’, then ‘Connections’ and select ‘Manage Stripe’ from the Stripe section.

3. Create an invoice

When you create an invoice, or recurring invoice profile, you'll see the option to accept online payments using Stripe.

When adding the invoice details, select 'Online payment options - Stripe' and then create the rest of your invoice as normal. You can use Stripe as a payment option for any invoice in a currency supported by your Stripe account.


When you are emailing your invoice, include an [online_payment_link] tag in the body of the email. This will embed an online payment link in the email that your customer will receive. This link will let your customer pay your invoice using a debit or credit card, via your Stripe account.

Please note the online payment link will only work if the invoice value is equal or greater to Stripe's current minimum fee.

How this works for your customers

When your customer receives your invoice via email, they can follow the online payment link you previously added to your email. This will show them your invoice, along with the option to pay by credit card via Stripe. Any other payment options you enabled while creating your invoice, such as PayPal, will also be available to them.


Receiving payments

Please note that your customer may need to go through 3D Secure 2 Strong Customer Authentication before they can make a payment for your invoice. As soon as a payment is made by your customer you should receive a confirmation email. This confirmation email will be sent to the email address of the registered account owner. Payments made with Stripe take seven days to appear in your bank account.

If a payment made with Stripe doesn't go through from your customer's account, it can be up to five days before Stripe is notified by the bank. While payments are pending or being processed, FreeAgent will stop sending automatic email reminders.

Stripe payment status

As soon as your customer has made a payment using Stripe, viewing your invoice will show a payment status of ‘Payment Processing' while FreeAgent waits for Stripe to confirm that the payment has been transferred to your account.


Finally, once the payment is transferred into your bank account you’ll see a 'Payment Complete’ status in the 'Stripe payment status' area.


Please note that when you see the ‘Payment Complete’ status, you still need to feed in or upload the transaction from your bank and explain it as an ‘Invoice Receipt’ against the invoice.

Failed payment

In the event that the transfer fails, you will see a 'Payment Failed’ status. This usually means that there was an issue with the bank account you have set up in Stripe. In this instance your client will still have been charged for your invoice. You should fix the issue with your bank account or get in touch with Stripe for more details. You can then retry the transfer from your Stripe dashboard.


How to account for Stripe fees in FreeAgent

For more information on how to account for automatically deducted Stripe fees in FreeAgent, please see this article.

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