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How to Accept WooCommerce SEPA Direct Debit Payments in Your Store

Updated:  Dec 23, 2025
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Author: Editorial Team
Editorial Team
Author: Editorial Team Editorial Team

The FunnelKit Editorial Team is a group of WooCommerce experts with 10+ years of combined experience. We create actionable guides based on hands-on testing, industry research, and user feedback to help eCommerce businesses grow.

How to Accept WooCommerce SEPA Direct Debit Payments in Your Store

If you are selling to customers in Europe, offering SEPA Direct Debit often becomes an expectation.

In 2024 alone, the euro area processed over 22.4 billion direct debit transactions worth €10.7 trillion, according to the European Central Bank's payment statistics. [Source: European Central Bank]

For WooCommerce store owners targeting the European market, SEPA Direct Debit removes the friction of cross-border payments and provides customers with a familiar, bank-based payment method.

In our experience optimizing thousands of WooCommerce checkout flows, we have seen that localising payment methods is one of the fastest ways to reduce cart abandonment.

SEPA Direct Debit consistently performs well for recurring payments and subscription-based businesses, where the "set it and forget it" nature of direct debits reduces involuntary churn.

In this article, we'll walk you through exactly how to set up WooCommerce SEPA payments using the Stripe Gateway plugin, including the specific configuration decisions we've found work best based on real-world implementations.

What is SEPA Direct Debit and Why Does It Matter for eCommerce?

The Single Euro Payments Area (SEPA) is a payment integration initiative that standardizes euro-denominated bank transfers across 36 European countries.

SEPA Direct Debit is regulated by the European Payment Council (EPC), which facilitates over 50 billion transactions in 41 countries every year.

SEPA Direct Debit allows businesses to collect payments directly from customers’ bank accounts, much like utility companies or subscription services do.

It uses the International Bank Account Number (IBAN) to identify bank accounts, the Business Identifier Code (BIC) to identify banks, and the common technical standards for payment messages.

Key statistics that demonstrate SEPA’s significance:

  • Direct debits account for 15% of all non-cash euro area transactions by volume (ECB, H2 2024).
  • SEPA Direct Debit Core represents 99% of all direct debits by volume in the eurozone.
  • Germany alone sees 17-23% of ecommerce purchases paid via direct debit, making it the third most popular online payment method in that market.
  • Settlement typically occurs within 2-3 business days, faster than international wire transfers.

Countries that accept SEPA Direct Debit payments:

SEPA covers 36 countries (27 EU member states plus 9 additional European nations). 

Understanding this geographic scope helps you assess whether SEPA should be a priority for your store.

EU Member States (27): Austria, Belgium, Bulgaria, Cyprus, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Poland, Portugal, Romania, Slovenia, Slovakia, Spain, and Sweden.

Non-EU SEPA Members (9): Andorra, Iceland, Liechtenstein, Monaco, Norway, San Marino, Switzerland, the United Kingdom, and Vatican City.

Why Offer WooCommerce SEPA Payments in Your Store?

Earlier, each European country had its own distinct payment protocols. SEPA was introduced to harmonize these financial and payment systems.

SEPA provides a standardized process for electronic payments across the EU and EEA, making transactions as easy as domestic ones.

It gained popularity as a smart bank redirect or local payment method to simplify cross-border payments within Europe.

In our experience working with stores that serve European markets, adding SEPA as a payment option delivers several measurable benefits:

  • Expanded market reach: SEPA enables you to reach customers across 36 European countries who prefer bank-based payments. In markets such as Germany and the Netherlands, direct debits and bank transfers are cultural norms. This helps you expand your potential customer base and tap into new markets.
  • Improved customer convenience: SEPA streamlines the payment process for customers within its zone. Customers can make direct payments from their bank accounts using IBAN and BIC, which are familiar and convenient payment methods in Europe.
  • Reduced cart abandonment: Customers who don’t have or don’t want to use credit cards can still complete purchases. This is particularly relevant for high-value orders where customers prefer bank security.
  • Faster settlement: SEPA payments offer faster settlement times than international wire transfers. This means you can quickly accept funds from SEPA transactions, improving your cash flow and liquidity.
  • Lower transaction costs: SEPA transactions typically carry lower processing fees than credit cards. Stripe’s SEPA pricing is generally more favourable than card rates, though this varies by country and volume.
  • Compliance with EU regulations: Accepting SEPA payments ensures compliance with EU regulations related to euro-dominated transactions. This can help you avoid potential legal issues related to non-compliance.
  • Enhanced trust and credibility: Offering WooCommerce SEPA payments can improve trust and credibility among European customers. It demonstrates that your business is committed to providing convenient and secure payment options tailored to their needs.

Integrating SEPA into your WooCommerce business contributes to smoother transactions, lower costs and improved customer satisfaction.

Essentials to Set Up WooCommerce SEPA Payment Method in Your Store

Before we set up the SEPA payment method in WooCommerce, let’s discuss the prerequisites you need for your store.

If you haven’t set up your WooCommerce business, here’s the official WooCommerce guide to help you.

1. A Stripe account

Stripe is a widely used online payment processing platform that enables businesses to accept payments over the web. 

Setting up your Stripe account is free, but they charge a small fee for each transaction. Its pricing fee structure varies by payment method and country.

Refer to this Stripe document to start collecting online payments in your store.

Make sure to enable SEPA from your Stripe payment dashboard.

2. Stripe Gateway for WooCommerce plugin

The Stripe Gateway for WooCommerce by FunnelKit offers a robust integration solution that facilitates seamless payments within your store.

Renowned as one of the top WooCommerce Stripe gateway plugins, it provides a straightforward and secure method for collecting payments on the web and mobile.

Stripe payment gateway for woocommerce plugin to set up sepa direct debit in the woocommerce store

It is compatible with all the major credit and debit cards such as Visa, Mastercard, American Express, Discover, JCB, Diners Club, etc. Additionally, it seamlessly integrates with express payment options such as Google Pay and Apple Pay.

Moreover, the plugin extends its compatibility to include various local payment methods such as iDEAL, SEPA, P24, Bancontact, and more.

This Stripe Gateway plugin seamlessly integrates with WooCommerce checkout pages and one-click upsells from FunnelKit. This way, it offers customers an effortless shopping experience.

3. A valid SSL certificate

An SSL certificate is crucial to secure your website, especially for eCommerce platforms like WooCommerce. It helps with website authenticity and encrypts data transmitted between a user’s browser and the server.

You should install a valid SSL certificate on your WooCommerce website.

4. Your store currency should be Euros (EUR)

Set the currency to EUR in your WooCommerce store.

Configure the currency to Euro (€) from WooCommerce general settings.

Set the woocommerce store currency to Euro to set up sepa direct debit

Save your changes when done.

How to Set Up and Configure WooCommerce SEPA Payments in Your Store?

Now that you have taken care of all your essentials, it’s time to connect Stripe with WooCommerce and enable SEPA Direct Debit payments in your store.

Follow the steps below to do so:

Step 1: Install the Stripe Gateway for WooCommerce plugin

Navigate to the Plugins section on your WordPress dashboard and search for “FunnelKit Stripe Gateway for WooCommerce”.

Next, install and activate it on your website.

Install and activate the stripe gateway for woocommerce plugin

Step 2: Connect Stripe with WooCommerce

Once the plugin is activated, click the ‘Start Onboarding Wizard’ button to start the WooCommerce-Stripe setup and configuration process.

Start the onboarding wizard to connect your stripe account with the woocommerce store - this is how you can set up woocommerce sepa in your store

It’ll open in a new window. From there, hit ‘Connect with Stripe’ to start the process.

It'll open a new window - from there click on Connect with Stripe

Enter your registered email address and password on the authorization page to log in to your Stripe account.

Enter the registered email address and password to log in to your Stripe account

Next, authenticate your Stripe account with a 6-digit verification code sent to your registered email or phone number.

Then, select the Stripe account you want to use for your WooCommerce SEPA integration.

Once done, click ‘Connect’.

Select your Stripe account and click on connect button to set up woocommerce sepa integration
  • Enable the payment gateways

On the next screen, you’ll see all the payment gateways enabled in your Stripe account. 

Hit the toggle next to the SEPA Direct Debit payment gateway.

Activate SEPA direct debit in woocommerce store
  • Set up webhook

The best thing about this Stripe Payment Gateway plugin is that it automatically sets up webhooks.

All you need to do is click on the ‘Setup Webhook Now’ button.

Set up webhook - it'll automatically configure webhook in your stripe account
  • Enable Express Checkouts

The next screen activates the express checkout buttons, such as Apple Pay and Google Pay.

Turn on the toggle to enable one-click checkouts in your WooCommerce store.

Enable express checkout like Apple Pay and Google Pay in your woocommerce store
  • Enable Stripe test mode

You’re all set! Activate the test mode and configure the WooCommerce Stripe SEPA payment option.

Put the stripe test mode and save all the settings

Now, the plugin will activate the Stripe test mode and automatically fetch all the account details into WooCommerce:

  • Stripe connection ID and status
  • Webhook ID and URL
  • Live and test webhook secret key
  • Debug log URL

Well done! You’ve successfully connected and configured the Stripe account in your WooCommerce store.

Step 3: Enable the SEPA Direct Debit in WooCommerce

Navigate to WooCommerce ⇨ Settings ⇨ Payments.

Navigate to woocommerce - settings - payments section

Under the Payments tab, scroll down and click on ‘Manage’ next to Stripe SEPA - SEPA Direct Debit.

Turn on the toggle to WooCommerce Stripe SEPA Direct Debit payment method

Click the checkbox next to ‘Enable Stripe SEPA Direct Debit’.

Enable the Stripe SEPA Direct Debit payment option in WooCommerce

This will enable the SEPA Direct Debit payment gateway in your WooCommerce store.

Step 4: Configure the WooCommerce SEPA payment option in your store

Customize the SEPA Direct Debit payment gateway from the following options:

Configure the WooCommerce SEPA direct debit payment option in your store
  • Title - The title of your SEPA payment gateway shown on the checkout page
  • Description - The description appears below the title of the SEPA payment method on the WooCommerce checkout page
  • Saved IBAN - Check this option to save IBAN details for future orders
  • Statement depositor - Name that appears on the customer’s statement in capital letters
  • Company name - The name of the company that will appear in the SEPA mandate information
  • Selling location - Set the SEPA selling location to the list of countries you wish to sell

Hit the ‘Save changes’ button when you’re done.

That’s it! You’ve successfully set up and configured the WooCommerce SEPA Direct Debit payment gateway in your store.

Testing the WooCommerce SEPA Payments in Your Store

To test the WooCommerce SEPA Direct Debit payment option, enable Stripe’s ‘Test’ mode from the WooCommerce payment settings.

Enable stripe test mode

Now, go to your shop page, add the item to the shopping cart, and head over to the checkout page.

Select the ‘SEPA Direct Debit’ payment option, enter the IBAN, and place the order now.

It’ll take a few seconds to authenticate your information.

Once done, it’ll direct you to the thank you page with a successful purchase.

WooCommerce thank you page preview

This is how you can test WooCommerce SEPA Direct Debit payments in your store.

After testing, change Stripe’s mode to ‘Live’ and you’ll be able to accept real payments via SEPA on your WooCommerce store.

Enhance Your WooCommerce SEPA Buying Experience with Beautiful Checkout Pages

The default WooCommerce checkout page is monotonous and solely focuses on completing the sale.

While it may suffice for some, it certainly lacks high-converting elements or offers to enhance average order value (AOV) and boost sales.

Default woocommerce checkout page

Imagine being able to craft stunning checkout pages with pre-designed templates that are optimized for conversions.

With just a few clicks, you can import and customize the checkout page templates effortlessly using any page builder - all without needing to code!

Here’s how you can modify the default checkout page into this:

High-converting woocommerce checkout page preview with all the elements

This custom checkout page has all the elements you need to drive sales and bring revenue, such as:

  • A multi-step checkout form that simplifies the checkout process and reduces cart abandonment.
  • The mini cart section lets shoppers view and adjust their cart contents on the checkout page. They can also apply a coupon code here.
  • Showcasing authentic customer testimonials helps build trust and credibility.
  • Order bump helps you maximize order value by presenting upsell offers at checkout.
  • The Shop with Confidence section helps instill trust and reassure shoppers, leading to higher conversion rates and increased customer satisfaction.
  • Reassure customers of a safe and secure shopping experience by prominently displaying the security badges on the checkout page.

You can create such high-converting checkout pages with FunnelKit Funnel Builder.

Not just that, this WooCommerce checkout manager plugin is capable of more than just customizing the page such as:

  • Checkout form field customization: Tailor the checkout form fields to match your business needs and customer preferences. Add custom fields, adjust the field labels, reorder the form layout, and more with a simple drag-and-drop!
  • Google address autocomplete: The Google Address Autocomplete feature simplifies address entry and improves data accuracy. It provides real-time suggestions and automatically completes the entire address once the user selects one.
  • Auto-apply coupons: Automatically apply discount coupons to the shopper’s orders. This way, you can enhance convenience for shoppers by taking advantage of available discounts, ultimately driving conversions and boosting sales.
  • Relevant product recommendations: Display relevant product recommendations during the checkout process. Offer relevant recommendations inside the shopping cart, on the checkout page, after the checkout as one-click upsells, or in post-purchase emails.

Watch this YouTube tutorial to set up profitable one-click upsells for your store:

How to Accept WooCommerce SEPA Direct Debit Payments in Your Store

So why wait? Get FunnelKit today and grow your business!

Bonus Tip: Unlock Revenue Potential with One-Click Upsells by Accepting Credit or Debit Card Payments

One-click or post-purchase upsells increase revenue by 35%.

Therefore, it’s important to elevate your sales strategy by setting up one-click upsell offers in your WooCommerce store.

These offers encourage customers to make additional purchases with a single click. There’s no need to fill out the details, as FunnelKit’s one-click upsells tokenize the payment method.

But keep in mind that not all payment gateways support one-click upsells.

You can add additional payment methods, such as Credit or Debit cards, to your WooCommerce store in addition to SEPA.

Credit cards offer much-needed convenience and flexibility, streamlining the checkout experience and potentially increasing impulse purchases.

You can enable card payments from the Stripe Gateway for the WooCommerce plugin.

To activate the credit card payment option, navigate to WooCommerce payment settings and enable the toggle next to Stripe Credit Card.

Enable Stripe credit card payment method in addition to WooCommerce SEPA direct debit

Configure the Credit card settings there:

Configure Stripe credit card payment gateway that accepts Visa, MasterCard, American Express, Discover, JCB, UnionPay, etc.

Click on ‘Save Changes’ when done.

Don’t forget to test the credit card payment if it shows on your WooCommerce checkout page along with SEPA.

Credit card payment method displayed on the checkout page

Once you’ve entered your credit card details, your upsell offer will be shown to you before the thank you page.

Post-purchase one-click upsell offers supported with credit card payments

You can even add multiple one-click upsells and link them according to whether your primary offer gets accepted or rejected.

Learn More: Refer to our detailed guide to set up one-click upsell offers in WooCommerce.

Frequently Asked Questions (FAQs)

In this section, we’ve answered some frequently asked questions related to WooCommerce SEPA:

How much time does it take for SEPA Direct Debit transactions to be processed?

The processing time for SEPA Direct Debit transactions varies depending on factors such as banking hours and the payment gateway's efficiency. Typically, it takes a minimum of two to three business days to process the payment.

Is WooCommerce SEPA available for businesses outside of Europe?

WooCommerce SEPA is primarily designed for businesses operating in the European market. SEPA enables cross-border Euro payments within the EU and to some non-EU countries. However, it only supports the Euro (EUR) currency. So, if your business is outside Europe but serves European customers, you can accept SEPA payments in your WooCommerce store.

Are there any additional fees associated with WooCommerce SEPA transactions?

Yes, there are fees associated with each WooCommerce SEPA transaction. This fee or pricing varies by region. But Stripe charges a small fee, which is nothing to worry about. Check out Stripe pricing for local payment methods here.

Can customers revoke SEPA Direct Debit mandates?

Yes, customers can revoke SEPA Direct Debit mandates at any time by contacting their bank. They must inform their bank in writing and indicate a reason for canceling the authorization. After that, the bank will notify the business of this cancellation and not collect any further payments.

Is WooCommerce SEPA compatible with mobile devices?

Yes, WooCommerce SEPA is compatible with mobile devices, allowing customers to pay conveniently using smartphones or tablets.

Does SEPA work with subscriptions?

Yes, the FunnelKit Stripe Gateway plugin supports product subscriptions, making SEPA an excellent choice for recurring payments. Once a customer authorises the initial mandate, subsequent subscription payments are collected automatically without requiring repeated customer action.

Why is SEPA not appearing on my WooCommerce checkout page?

SEPA payments only work with euro (EUR) transactions. First, make sure your store currency is set to EUR in WooCommerce settings. Next, confirm that SEPA Direct Debit is enabled in your Stripe Dashboard under Payment Methods.

Why are SEPA payments failing for customers in certain countries?

This typically happens due to restricted Selling Location settings in WooCommerce. Check that SEPA-supported countries are not accidentally excluded from your allowed selling regions.

Are You Ready to Accept SEPA Direct Debit Payments in Your WooCommerce Store?

Adding SEPA Direct Debit to your WooCommerce store is a strategic decision for any business serving European customers.

With over 22 billion transactions processed annually and coverage across 36 countries, SEPA represents a significant opportunity to reduce friction in your checkout process and meet customer payment preferences.

The setup process itself is straightforward and takes 15 to 20 minutes with the right tools.

The FunnelKit Stripe Gateway simplifies technical configuration, particularly webhook management, and integrates seamlessly with optimised checkout pages.

From expanding your market reach to enhancing security and streamlining transactions, the SEPA Direct Debit payment method is designed to help you thrive in the competitive eCommerce landscape.

Furthermore, you can add SEPA Direct Debit to your beautiful custom checkout pages and drive massive conversions!

So what are you waiting for?

Get set to take the next step and accept WooCommerce SEPA Direct Debit payments in your store.

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Published by: Editorial Team
The Editorial Team at FunnelKit (formerly WooFunnels) is a passionate group of writers and copy editors. We create well-researched posts on topics such as WordPress automation, sales funnels, online course creation, and more. We aim to deliver content that is interesting and actionable.
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