EMA Guidance: SEPA Direct Debit B2B for Applicants and Marketing Authorisation Holders

Sharan Murugan
17 hours ago
3 min read

The European Medicines Agency (EMA) has issued guidance explaining how applicants and marketing authorisation holders can use SEPA Direct Debit Business-to-Business (B2B) to pay certain EMA fees. The guidance, dated 20 August 2026, covers mandate setup, payment collection, returned transactions, withdrawals and related requirements.

Single Euro Payments Area framework (SEPA) Direct Debit B2B allows EMA to collect euro-denominated payments from business debtors using a signed mandate. It is currently available only for prepayment invoices relating to Scientific Advice, Certificates and Parallel Distribution.

Setting Up the SEPA Direct Debit B2B Mandate

Applicants and marketing authorisation holders must have an EMA customer account and complete and sign a SEPA Direct Debit B2B mandate. The payer must provide accurate legal entity and bank information, including the EMA customer account number, account holder name, IBAN and BIC. A separate mandate is required for each legal entity with an EMA customer account, even when entities share a bank account.

An authorised representative must sign the mandate. Once received, EMA activates the mandate, assigns a unique mandate reference and communicates it to the payer. The payer must then register the mandate with its bank before the first collection.

Eligible EMA Services

SEPA Direct Debit B2B is currently available only for Scientific Advice, Certificates and Parallel Distribution.

Payers can choose to use direct debit for selected eligible services while continuing to pay other invoices by bank transfer. The selected services should be communicated to EMA upon submission of the mandate.

Pre-Notification and Payment Finality

EMA provides 14 days' advance notice of collections unless another arrangement has been agreed. For the services covered by the guidance, the invoice serves as the pre-notification and informs the payer that EMA may submit the collection instruction on the following business day.

Payment is not immediately final after the payer's account is debited. The payer's bank may return a transaction for scheme-defined reasons within three TARGET business days. Once this period expires, the payment becomes final and irrevocable, and EMA considers it received.

The three-business-day period refers to TARGET business days, rather than calendar days or necessarily local working days.

Returned Transactions and Service Delays

Transactions may be returned because of issues such as an unregistered or mismatched mandate, a closed or blocked account, insufficient funds depending on bank policy, or technical or processing errors.

If payment is returned, the prepayment condition is not fulfilled, and EMA may be unable to provide the related service until successful payment has been received and becomes final. Applicants should ensure that mandates are correctly registered, sufficient funds are available, and account details remain accurate.

Where collection fails, an alternative payment such as bank transfer may be required. If payment is not received by the invoice due date, 30 calendar days from the invoice date, the invoice and application may be cancelled and an administrative charge may apply.

Withdrawals and Duplicate Payments

EMA cannot stop a direct debit collection once the instruction has been submitted to the bank for processing.

For certificates and parallel distribution applications, changes, cancellations or withdrawals are not accepted once the request has been submitted and relevant fees have been paid in full. Scientific Advice requests have separate withdrawal rules depending on when the request is withdrawn.

EMA does not maintain two payment methods for the same payer, service and invoice. A subsequent payment for an invoice already collected through SEPA Direct Debit B2B is treated as a duplicate and returned.

Mandate amendments or cancellations should be communicated to EMA's accounts team. Repeated failed collections may lead EMA to request termination of the mandate.

Charges and Internal Coordination

EMA offers the SEPA Direct Debit B2B service free of charge, but may recover charges resulting from returned transactions.

The guidance recommends coordination between regulatory and financial teams, particularly for invoice approval processes and the transition between payment methods.

Key Steps for Applicants and MAHs

The EMA checklist highlights the need to:

Maintain an active EMA customer account.
Confirm eligibility of the business bank account for SEPA B2B.
Use the official EMA mandate template.
Complete legal entity and bank details accurately.
Provide one mandate for each legal entity.
Obtain an authorised signature.
Submit the signed mandate to EMA.
Register the mandate with the payer's bank.
Ensure sufficient funds are available.
Inform EMA when bank registration is complete.

The guidance was issued on 20 August 2026 and includes a setup checklist and communication templates for applicants and marketing authorisation holders.