Automate SEPA Direct Debits in Shopify: Say Goodbye to Excel Spreadsheets and Manual Debits

Anyone who runs a Shopify store in the DACH region—especially in B2B—is familiar with the problem: Customers want to pay by direct debit, but Shopify doesn’t offer a native, fully automated solution for this. The result is Excel spreadsheets full of IBANs, manual direct debit entries in the banking tab, and shipping approvals that sit idle for days waiting for funds to come in. In this article, we’ll show why SEPA direct debit is the most cost-effective payment method—especially for B2B and repeat-customer stores—and how the entire process can be automated with SepaGo.

Why SEPA Direct Debit Is So Attractive for Shopify Merchants

SEPA Direct Debit is one of the most popular payment methods in German-speaking countries—and, from a merchant’s perspective, one of the most cost-effective. While credit cards and PayPal take a percentage of the cart total, a direct debit typically costs only a few cents to a few euros. The difference becomes even greater as the order value increases:

Especially in B2B, where shopping carts can total several hundred or thousand euros, the savings add up quickly: A store with 100 orders per month and an average cart value of €200 saves about €305 per month compared to credit card payments—over €3,600 per year.

The problem: Shopify doesn’t natively support direct debit

Shopify Payments does not support SEPA Direct Debit in the DACH region as a fully-fledged, automated payment method for recurring orders. In practice, many merchants therefore resort to a manual workaround:

1. The customer places an order on account or selects “Prepaid Direct Debit”

2. The merchant requests the IBAN via email or enters it into an Excel list

3. The direct debit is initiated manually via online banking

4. Returned payments must be followed up on manually

5. Shipping is delayed until the funds are visibly received

This takes an average of about 5 minutes per order—and doesn’t scale. With 300 direct debit orders per month, that amounts to 25 work hours wasted in the back office. Added to this is the compliance risk: IBANs stored in Excel files and email inboxes are a nightmare from a GDPR perspective.

The solution: SepaGo – SEPA direct debit on autopilot

SepaGo is a Shopify app that fills exactly this gap. The app connects the Shopify checkout with GoCardless, Europe’s largest direct debit specialist—and automates the entire collection process. The concept can be summed up in one sentence: Set up the mandate once, and every subsequent order is collected automatically.

Here’s how SepaGo works in four steps

1. The customer selects SEPA at checkout. The direct debit appears as a native payment method directly in the Shopify checkout—without any plugin workarounds.

2. Mandate via GoCardless. The customer grants their SEPA mandate once in a hosted GoCardless flow. The IBAN and BIC are sent directly to the payment specialist, never to the store or to SepaGo.

3. Automatic follow-up collection. For every subsequent order, SepaGo collects the amount automatically. No clicks, no re-authentication, no follow-up phone calls.

4. Status displayed live in Shopify. Whether paid, failed, or pending—the payment status appears in real time in the Shopify backend. Shipping can be managed according to your own rules, even on the same day if desired.

For merchants, this feels like a standing order—except that billing is based on actual orders, not a flat monthly fee.

The pricing model: capped rather than percentage-based

SepaGo charges a flat fee of €0.30 plus 1% of the order value—with the percentage capped at €1. The maximum fee is €1.30 per order, regardless of whether the shopping cart total is €100 or €3,000. There is no monthly base fee, no setup costs, and no minimum contract term. You only pay when funds are actually transferred—and there’s a 30-day money-back guarantee.

This is precisely where the biggest advantage lies for B2B stores: A €3,000 wholesale order incurs a fee of €1.30, whereas providers that charge a percentage would bill €60 or more.

Security: Bank details remain with GoCardless, not with the store

A key point for many merchants: SepaGo is deliberately built as a pure integration layer. The app orchestrates the process between Shopify and GoCardless—sensitive data never touches the SepaGo servers.

• IBAN and BIC are stored exclusively with GoCardless, an FCA-regulated and PCI-DSS Level 1-certified payment provider.

• SepaGo only sees the mandate ID and status (active, collected, failed)—in the event of a hypothetical data breach, there would simply be nothing to steal.

• AES-256 encryption for all sensitive login credentials—the same standard used by banks.

• GDPR-compliant: The servers are located directly at GoCardless in the United Kingdom, which is considered a safe third country for data protection purposes thanks to the EU Adequacy Decision.

For online stores that have previously managed IBANs in Excel spreadsheets, this is not only a convenience upgrade but, above all, a compliance upgrade.

Direct Debit or Bank Transfer? The Right Payment Method for Each Target Group

SEPA Direct Debit really shines where trust already exists: with regular customers, repeat buyers, and in B2B. For first-time buyers in B2C, however, the risk of chargebacks is higher. That’s why SepaGo covers both scenarios:

• SEPA Direct Debit for B2B & regular customers: Fully automated collection, capped fees, and dispatch control based on trust level. Ideal for wholesale, repeat customers, and subscription-like models with high-value shopping carts.

• SEPA Credit Transfer for B2C & New Customers: Traditional prepayment—collect payment first, then ship. No chargeback risk, no outstanding balance. Ideal for first-time orders and high-value orders from new customers.

Both options run through a single app and backend—the merchant decides which payment method appears at checkout for each target group.

Full control: Who actually sees the direct debit option at checkout?

A common objection to offering direct debit in an online store is: “I don’t want to offer this to everyone.” That’s exactly why SepaGo provides three levels of control that let you precisely determine when SEPA appears at checkout—and when it doesn’t.

1. Country-based control: SEPA only where it makes sense

In the backend, you can specify for each country whether SEPA Direct Debit is offered at checkout. This payment method appears only if the shipping address is located in an enabled country. By default, all 27 EU member states are enabled—from Germany and Austria to France and Sweden. The EEA countries (Iceland, Liechtenstein, Norway) as well as other SEPA participants such as Switzerland, the United Kingdom, Monaco, San Marino, Andorra, and Vatican City can be optionally enabled.

This means SepaGo covers the entire SEPA area—but merchants decide for themselves whether they want to serve only the DACH region, for example, or collect payments EU-wide.

2. Customer Groups: Direct Debit for B2B Merchants Only

Using Shopify Customer Tags, you can restrict the visibility of this payment method to specific customer groups. A typical setup: Only customers with the “B2B” or “Wholesale” tag see SEPA Direct Debit at checkout—and only if they are logged in. Walk-in customers and first-time buyers are not shown this payment option at all.

The tags are managed directly in Shopify under Customers → Tags; multiple tags can be combined. Without any restrictions, direct debit remains visible to all customers. For B2B stores that want to use direct debit specifically as a privilege for verified merchant accounts, this is the most elegant solution—without the need for a separate wholesale channel.

3. Address Verification: Built-in Fraud Protection

When the first SEPA direct debit is successfully processed, SepaGo saves the customer’s billing address as a reference. If the shipping or billing address differs in a subsequent order, the direct debit is automatically paused and the customer is asked to confirm via email. Only then is the payment processed.

This protects against a classic fraud pattern: A compromised customer account suddenly places an order to an unfamiliar address—and the direct debit goes through anyway. With address verification enabled, this doesn’t happen. For B2B customers who regularly place orders to multiple shipping addresses (such as different warehouses), the verification can be selectively disabled so that legitimate orders aren’t mistakenly blocked.

Who Benefits from SepaGo?

SepaGo is built for Shopify stores in the DACH region, specifically:

• B2B retailers and wholesalers with recurring orders and high-value shopping carts

• Stores with a large base of repeat customers that want to reduce friction at checkout

• Subscription-based business models that bill per order rather than at a flat rate

• Merchants who have been collecting payments manually and want to reclaim back-office time

The app is Built-for-Shopify certified (in the certification process), Shopify Plus compatible, and an official GoCardless partner. Behind SepaGo are two German teams from the Shopify ecosystem—Labrigart Design GmbH and AP10 Studios—with many years of experience in CRO and store migration.

Conclusion: Direct debit without manual effort

SEPA Direct Debit is the most cost-effective payment method for recurring orders in the DACH e-commerce market—but until now, it has involved a lot of manual work. SepaGo automates the entire process from mandate setup to subsequent collections, securely stores bank details with GoCardless, caps the fee at €1.30 per order, and provides built-in control mechanisms such as country-specific settings, customer group approvals, and address verification. For B2B shops and merchants with a base of regular customers, this is one of the fastest ways to reduce payment fees and reclaim back-office time.