Process Engineer

Amylyx has an audacious mission to usher in a new era for treating diseases with high unmet needs. Where others see challenges, we see opportunities that we pursue with urgency, rigorous science, and unwavering commitment to the communities we serve. We are a clinical-stage company currently focused on post-bariatric hypoglycemia (PBH), Wolfram syndrome, and amyotrophic lateral sclerosis (ALS).

Our mission is powered by our people. Our core values – be audacious, be curious, be authentic, be engaged, and be accountable – creating a culture of caring. Amylyx has assembled an experienced team ready to take action because the communities we serve have no time to wait. If you share our passion and are determined to tackle some of medicine’s toughest problems, we encourage you to read the opportunity below and apply.

The Opportunity

The Process Engineer, Drug Product, will provide technical and GMP support for contract manufacturing organizations (CMOs) responsible for late-stage clinical and commercial drug product supply. This role serves as the primary technical subject matter expert (SME) for aseptic processing including sterile filtration, formulation, filling, and container closure systems. The role will establish and maintain strong, trust-based relationships with CMO technical and quality teams to ensure reliable, compliant, and efficient manufacturing of aseptically filled drug products. Operating as a highly agile technical expert, partnering with CMOs and internal stakeholders to ensure robust execution across technology transfer, validation, and lifecycle management. This role reports to the Associate Director, CMC Drug Product.

Responsibilities

Commercial & Clinical Aseptic Manufacturing Support:

• Support technical leadership and day‑to‑day aseptic process engineering support for clinical and commercial drug product manufacturing at external CMOs.


• Serve as the aseptic processing SME during manufacturing operations providing onsite support when required.


• Lead investigations, perform rigorous root cause analysis and develop scientifically sound CAPAs, ensuring alignment with regulatory expectations and industry best practices.


• Assess and author technical risk assessments and change controls to support manufacturing changes, investigations, and regulatory filings.


• Ensure strict compliance with cGMPs, global regulatory requirements, and internal quality systems for aseptic manufacturing.

Process Validation & Product Launch

• Lead and support aseptic drug product technology transfer activities from development to clinical and commercial manufacturing sites.


• Define and transfer critical process parameters (CPPs), critical quality attributes (CQAs), and in‑process controls for aseptic unit operations.


• Develop and execute aseptic process validation strategies, including PPQ planning, statistical sampling plans, and acceptance criteria aligned with regulatory guidance.


• Provide technical authorship and review for regulatory submissions (IND, BLA, NDA, MAA), validation reports, and responses to regulatory agency questions.


• Support new product introductions and commercial launches by ensuring validated, scalable, and inspection‑ready aseptic processes.

Data Analysis & Continued Process Verification

• Lead continued process verification (CPV) and routine data trending for aseptic unit operations, environmental monitoring, and critical process parameters.


• Develop and maintain data repositories, dashboards, and meaningful KPIs to assess aseptic process capability and performance.


• Identify early signals of process drift or increased contamination risk and proactively drive corrective or preventive actions.


• Prepare and present quarterly CPV summaries and technical assessments for internal management reviews.

Continuous Improvement

• Identify and execute continuous improvement initiatives focused on aseptic process robustness, sterility assurance, capacity, and operational efficiency.


• Apply Quality by Design (QbD), statistical tools, and risk‑based decision making to optimize aseptic manufacturing processes.


• Collaborate with CMOs to implement best practices, new technologies, or process enhancements where appropriate

Required Qualifications

• Bachelor’s degree in engineering or related field with 5+ years/ Master’s with 3+ years of relevant experience.


• Prior experience in aseptic drug product manufacturing for late-stage development/commercial is required. Device experience is a plus.


• Proficiency in Quality by Design (QbD), Design of Experiments (DoE), statistical process control (SPC), and complex data analysis.


• Familiarity with modeling and optimization tools (e.g., MATLAB, JMP) is a plus.


• Detail-oriented with strong problem-solving skills and ability to identify subtle trends in data.


• Comprehensive understanding of cGMP principles and regulatory requirements, including process, equipment, and facility validation.


• Excellent communication and teamwork skills.


• Ability to travel to domestic and international CMOs as needed.

Work Location and Conditions

• At Amylyx, we proudly support remote work opportunities within the United States. However, due to business considerations related to health insurance coverage and state tax regulations, we are unable to hire employees who reside and/or work in certain states. Currently, we are not considering applicants from Alaska, Arizona, Hawaii Michigan and Tennessee.


• You will be expected to travel to our corporate location in Cambridge, MA several times a year and attend other company-related events as necessary and requested.


• You must have access to work in setting which enables meeting all requirements of the role (including privacy, reliable internet access, phone, ability to video conference, etc.) at your remote location.

To stay connected with us, follow Amylyx Pharmaceuticals on LinkedIn.

To return to our website please click here.

Amylyx Pharmaceuticals is an Equal Opportunity Employer that does not discriminate on the basis of actual or perceived race, color, creed, religion, national origin, ancestry, citizenship status, age, sex or gender (including pregnancy, childbirth, pregnancy-related conditions, and lactation), gender identity or expression (including transgender status), sexual orientation, marital status, military service and veteran status, physical or mental disability, genetic information, or any other characteristic protected by applicable federal, state, or local laws and ordinances. Amylyx’s management team is dedicated to this policy with respect to recruitment, hiring, placement, promotion, transfer, training, compensation, benefits, employee activities, access to facilities and programs, and general treatment during employment. Accommodations are available for candidates who require them in our selection process. If you need an accommodation, please let your Amylyx Talent Acquisition contact know.

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.