Quanterix Corp

Evaluation of Disclosure Controls and Procedures

We have established disclosure controls and procedures (as such term is defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act) that are designed to provide reasonable assurance that information required to be disclosed in the reports we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in the rules and forms of the SEC and to ensure that such information is accumulated and communicated to management, including our Chief Executive Officer (principal executive officer) and Chief Financial Officer (principal financial officer), to allow timely decisions regarding required disclosures.

Under the supervision and with the participation of our management, including our Chief Executive Officer and Chief Financial Officer, we conducted an evaluation of the effectiveness of our disclosure controls and procedures as of

December 31, 2025. Based on this evaluation, our Chief Executive Officer and Chief Financial Officer concluded that our disclosure controls and procedures were effective as of December 31, 2025.

Management’s Report on Internal Control over Financial Reporting

Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as this term is defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act. Our internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. All internal control systems, no matter how well designed, have inherent limitations. Therefore, even those systems determined to be effective can provide only reasonable assurance with respect to financial statement preparation and presentation.

Under the supervision and with the participation of our management, including our Chief Executive Officer (principal executive officer) and Chief Financial Officer (principal financial officer), we conducted an evaluation of the effectiveness of our internal control over financial reporting as of December 31, 2025, based on the framework set forth in Internal Control-Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (the "2013 Framework"). Based on our evaluation under the 2013 Framework, management concluded that our internal control over financing reporting was effective as of December 31, 2025.

The foregoing evaluation excludes our acquisition of Akoya Biosciences, Inc. ("Akoya") on July 8, 2025 (refer to Note 3 - Acquisitionsin the Notes to Consolidated Financial Statements). The acquisition of Akoya was accounted for as a business combination and Akoya's operating results have been included in our Consolidated Financial Statements since the acquisition date. In accordance with guidance from the staff of the SEC, companies are permitted to exclude acquisitions from their evaluation of internal control over financial reporting for the first year after an acquisition. Akoya represented approximately 43% of the Company's total assets, excluding the preliminary value of goodwill, and 24% of the Company's total revenues as of and for the year ended December 31, 2025.

The Company’s independent registered public accounting firm, KPMG LLP, has also issued an audit report on the Company’s internal control over financial reporting, which is included elsewhere in this Annual Report on Form 10-K.

Remediation of Previously Identified Material Weaknesses

In preparing our financial statements in connection with our Annual Report on Form 10-K for the year ended December 31, 2024 and continuing through the nine months ended September 30, 2025, we previously identified and disclosed material weaknesses in our internal controls associated with the valuation of inventory, including excess and obsolescence reserves and the capitalization of labor and overhead costs and the accounting for Accelerator Laboratory revenue, a component of our service and other revenue.

Following the identification of the material weaknesses, and with the oversight of our audit committee, we commenced remediation efforts which continued during fiscal 2025 to address the material weaknesses and enhance our control environment, including our internal control over financial reporting. Our remediation efforts included:

•hiring a Vice President, SOX Transformation and personnel for our internal SOX Transformation team. This team:

◦oversaw the remediation of our material weaknesses and improvements across our internal controls;

◦evaluated and designed effective and scalable internal controls, and strengthened the documentation of our existing controls;

◦established new internal controls evaluating the accounting for inventory and enhanced inventory valuation review procedures;

◦enhanced and expanded our existing revenue recognition control procedures and attributes to sufficiently document our assessment of, and reviews over, information used to record Accelerator Laboratory revenue; and

◦provided trainings on a regular basis related to internal control over financial reporting for all control owners.

•implementing new software solutions to automate key manual inventory valuation processes and outputs;

•designing and implementing new controls;

•bringing additional internal systems into the scope of our internal control environment to reduce reliance on manual processes and controls;

•continued execution of controls that we worked to improve during fiscal year 2024 that did not have a sufficient period of time to demonstrate operating effectiveness as of December 31, 2024, including the analysis of labor and overhead cost capitalization and related controls implemented in the fourth quarter of 2024; and

•evaluating, enhancing, and adding personnel in the finance organization with a focus on the requisite experience in the areas of accounting, SEC financial reporting, and internal control compliance.

Based on these remediation actions, as well as testing the operating effectiveness of the applicable financial reporting controls over a sustained period of financial reporting cycles, we have concluded that all previously reported material weaknesses have been effectively remediated as of December 31, 2025.

Changes in Internal Control over Financial Reporting

Other than the changes outlined related to the remediation of the material weaknesses described above, there have been no changes in our internal control over financial reporting during the fiscal quarter ended December 31, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.