MetaVia Inc.

Evaluation of disclosure controls and procedures

As required by Rules 13a-15(b) and 15d-15(b) under the Section 21E of the Securities Exchange Act, our management, with the participation of our principal executive officer (“PEO”) and principal financial officer (“PFO”), evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act) as of the end of the period covered by this Report. Based upon that evaluation, our PEO and PFO concluded that our disclosure controls and procedures were effective as of the end of the period covered by this Report.

Previously identified material weaknesses in internal control over financial reporting

In connection with the preparation of the financial statements included in our 2024 Form 10-K, management identified the following material weaknesses:(i) logical access over the accounting software and (ii) lack of review over reconciliation of accrued clinical trial liabilities. A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of our annual or interim financial statements will not be prevented or detected on a timely basis. See “Remediation efforts to address the material weaknesses” below for steps we had taken to correct these material weaknesses.

Remediation efforts to address the material weaknesses

Under the oversight of the audit committee, management developed a detailed plan and timetable for the implementation of appropriate remedial measures to address the material weaknesses. As of June 30, 2025, the following actions have been taken:

As of June 30, 2025, management has concluded that the actions described above were satisfactorily implemented and have been in place for a sufficient period of time to demonstrate that the previously identified material weaknesses have been remediated.

Inherent limitations of disclosure controls and procedures

Our management, including our PEO and PFO, does not expect that our disclosure controls and procedures will prevent all errors and all fraud. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute,

assurance that the objectives of the control system are met. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within the Company have been detected. These inherent limitations include the realities that judgments in decision-making can be faulty, and that breakdowns can occur because of a simple error or mistake. Additionally, controls can be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the control. The design of any system of controls is also based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Over time, controls may become inadequate because of changes in conditions, or the degree of compliance with the policies or procedures may deteriorate. Because of the inherent limitations in a cost-effective control system, misstatements due to error or fraud may occur and not be detected.

Changes in internal control over financial reporting

Other than the remediation activities listed above for previously identified material weaknesses in internal control over financial reporting, there have been no other changes in our internal control over financial reporting during the quarter ended June 30, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.