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 and how this works for your customers.

The benefits of using Stripe include:

  • allowing your customers to easily pay invoices online by sending them a payment link
  • allowing your customers to pay for invoices by debit or credit card
  • optimised checkout options for your customers including Apple Pay, Google Pay and Stripe 1-click checkout
  • ability to customise the Stripe checkout portal with your own branding

Find out about Stripe charges.

You can also collect invoice payments online using PayPal, GoCardless or Tyl by NatWest. Find out more about payment solutions in FreeAgent.

Setting up Stripe in your FreeAgent Account

1. Enable Stripe

Navigate to the drop-down menu at the top-right of the screen and select ‘Connections & Add-ons’.

Connections and add-ons highlighted within drop-down menu

Select 'Learn more' in the 'Stripe' section.


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 disconnect 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, select the 'Stripe' checkbox in the 'Payments' section and 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.

If you'd like Stripe to be selected by default when creating future invoices, find out how to set up default payment settings.


When you are emailing your invoice, select the checkbox next to 'Include online payment button below content' or 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 that:

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

  • if a bank transaction is explained against the invoice before your customer makes the payment, when they select the payment link they’ll only be able to pay the remaining balance of the invoice, not the full amount.

  • if you use Stripe’s Instant Payout feature for an invoice created in FreeAgent, you’ll need to manually explain the bank transaction as a payment for the invoice. Alternatively, you can share the payment link with your customer rather than sending them the invoice.


How this works for your customers

When your customer receives your invoice via email, they can select the 'View and pay' button that you previously added to your email.

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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.


Your customer will then be taken to Stripe's checkout portal which will provide them with options to pay the invoice using Apple Pay, Google Pay, Stripe 1-click checkout or enter their card details.

You can customise the checkout portal with your own branding via your Stripe Dashboard. Find out more about how to customise the Stripe checkout portal.

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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, find out how to split a transaction for commission or charges deducted.

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