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Downstream Process Engineer Jobs (NOW HIRING)

The ideal candidate brings hands-on experience in biotech or pharmaceutical process engineering, with a focus on upstream, downstream or cell therapy operations. Key Responsibilities Support the ...

Senior Manager, Process Engineering

Durham, NC · On-site

$114.10K - $211.90K/yr

Provide technical expertise on biologics process equipment across upstream and downstream ... Experience in process engineering or manufacturing science within biologics or pharmaceutical ...

Role OverviewThe Principal Scientist, Lentivirus Downstream Process Development, will be a key ... RequirementsAdvanced degree (PhD preferred, or MS) in Chemical Engineering, Biomedical Engineering ...

The ideal candidate brings hands-on experience in biotech or pharmaceutical process engineering, with a focus on upstream, downstream or cell therapy operations. Key Responsibilities Support the ...

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Downstream Process Engineer information

See salary details

$49.5K

$92K

$142.5K

How much do downstream process engineer jobs pay per year?

As of Jun 1, 2026, the average yearly pay for downstream process engineer in the United States is $92,018.00, according to ZipRecruiter salary data. Most workers in this role earn between $74,500.00 and $103,000.00 per year, depending on experience, location, and employer.

What are the key skills and qualifications needed to thrive as a Downstream Process Engineer, and why are they important?

To thrive as a Downstream Process Engineer, you need a solid background in chemical or biochemical engineering, experience with purification processes, and often a relevant engineering degree. Familiarity with chromatography, filtration systems, process simulation software (like Aspen or MATLAB), and cGMP regulations is typically required. Strong problem-solving, analytical thinking, and communication skills enable effective troubleshooting and collaboration with cross-functional teams. These skills are crucial for optimizing product yield, ensuring regulatory compliance, and maintaining efficient and safe manufacturing operations.

What are some common challenges faced by Downstream Process Engineers when scaling up bioprocesses from lab to production?

One of the key challenges for Downstream Process Engineers is ensuring that purification and separation processes developed at the lab scale remain efficient and cost-effective during large-scale production. Factors such as changes in equipment performance, increased impurity loads, and process consistency can complicate scale-up. Engineers must also collaborate closely with upstream teams, quality assurance, and manufacturing staff to troubleshoot issues and optimize yield and product quality. Effective communication and adaptability are essential for overcoming these challenges and ensuring a smooth transition from development to manufacturing.

What is a Downstream Process Engineer?

A Downstream Process Engineer is a professional who specializes in the purification and processing of biological products, such as proteins or pharmaceuticals, after the initial production phase. Their main responsibility is to develop, optimize, and manage processes that separate and refine products from mixtures, ensuring quality and efficiency. This typically involves techniques like filtration, chromatography, and centrifugation. Downstream Process Engineers work closely with other scientists and engineers to scale up processes for commercial manufacturing while maintaining safety and regulatory compliance.

What is the difference between Downstream Process Engineer vs Upstream Process Engineer?

AspectDownstream Process EngineerUpstream Process Engineer
Primary FocusPurification, separation, and finishing of bioproductsCell culture, fermentation, and biomass production
Skills & CertificationsBioprocessing, chromatography, filtration, GMP knowledgeBioreactor operation, microbiology, fermentation techniques
Work EnvironmentManufacturing facilities, labs, quality controlResearch labs, pilot plants, production facilities
Industry UsageBiotech, pharmaceutical manufacturingBiotech, pharmaceutical, agricultural biotech

Both roles are essential in bioprocessing, with downstream process engineers focusing on product purification and upstream process engineers on initial bioproduction. Understanding their differences helps in career planning and job search strategies within the biotech industry.

More about Downstream Process Engineer jobs
Infographic showing various Downstream Process Engineer job openings in the United States as of May 2026, with employment types broken down into 33% Full Time, and 67% Contract. Highlights an 100% In-person job distribution, with an average salary of $92,018 per year, or $44.2 per hour.
Principal Scientist, Downstream Process Development

Principal Scientist, Downstream Process Development

Merck & Co., Inc.

Rahway, NJ • On-site

Full-time

Medical, Dental, Vision, Retirement, PTO

Posted 18 days ago


Merck rating

7.8

Company rating: 7.8 out of 10

Based on 50 frontline employees who took The Breakroom Quiz

41st of 71 rated pharmaceutical


Job description

Job Description
BPR&D within our Company's Research Laboratories is on a mission to rapidly deliver biotherapeutics to patients by efficiently developing innovative, robust manufacturing processes and technologies. To achieve this, we work closely with colleagues in Discovery, Pre-clinical, Early Development, Analytical, Formulation, and Commercial Manufacturing while providing an inclusive environment for all. Beyond process development for pipeline biologics, we innovate and build next generation biomanufacturing technologies. Examples include investments for development of continuous manufacturing, green and sustainable processes, and proprietary technology platforms. We actively publish and engage with the scientific community to influence the field.
As a Principal Scientist you will have the opportunity to influence the future direction of our Company's Downstream Processing of Biologics. You will work with an immensely creative and collaborative team of scientists and engineers to design purification processes while developing technical strategies related to downstream processing for drug candidates in early- and late-stage development.
Responsibilities include but are not limited to:
• As an impactful contributor, shape and realize innovation across the Biologics' pipeline, strategy, and science
• Advance the pipeline by collaborating with cross-functional teams, from Research & Manufacturing, in a fast-paced, multidisciplinary environment
• Participate in or lead 1) development of robust and scalable purification processes for biologics in different stages of clinical development, 2) process characterization and regulatory filings for successful commercialization
• Advance downstream processes by improving efficiency and cost effectiveness through research and innovation, while assessing technologies and industry best practices
• Collaborate with academia, industry, and vendors to drive development and early adoption of novel process technologies
• Contribute to strategic initiatives; partner with senior leaders to set overall project strategy, and guide teams towards its execution
• Conceptualize, plan, and execute projects with effective organizational, prioritization and problem-solving skills
• Stay abreast of scientific and regulatory landscape; actively present (premier conferences), publish (peer-reviewed journals) and patent
• Represent BPR&D as a downstream bioprocess expert in internal, cross-functional project teams and external conferences/consortia
• Mentor and actively share expertise; guide career development; build strong, collaborative teams
• Champion compliance and safety; promote a culture of inclusion
MINIMUM EDUCATION REQUIREMENTS:
Ph.D. with 6+ years, MS with 8+ years, or BS with 10+ years of industry experience and background in Chemical/Biochemical engineering, or a related field
REQUIRED EXPERIENCE, SKILLS, AND COMPETENCIES
• Strong fundamental knowledge and subject matter expertise in downstream processing of biologics, recent advances, and challenges in the field
• Expertise in independently conducting and directing the design, execution, analysis, and documentation of all stages of purification process development
• Track record of accomplishments in downstream bioprocessing with a history of peer-reviewed publications and presentations
• Knowledge of biologics CMC development
• Adaptability and agility to prioritize and deliver complex objectives, often on tight timelines, in a rapidly changing environment
• Experience and aptitude to lead, work, and collaborate in internal and external cross-functional, matrixed teams
• Action-oriented, mindset for creativity; ability to take initiative, innovate, iterate and problem-solve
• Demonstrated commitment to coach and mentor staff to maximize talent development and utilization
• Excellent interpersonal and communication skills
PREFERRED EXPERIENCE & SKILLS:
• Leadership of CMC development teams
• Continuous biomanufacturing integrated with process-analytical technologies
• High-throughput experimentation, automation, and process control
• Knowledge of protein expression, analytics, conjugation chemistry and formulation
• Biophysical, mechanistic and facility modeling; statistical analysis, data-science, machine learning, artificial intelligence
Required Skills:
Adaptability, Adaptability, Artificial Intelligence (AI), Biomanufacturing, Bioprocess Engineering, Career Development, Cell Culture Process Development, Cell Line Development, Combination Products, Data Analysis, Finite Element Analysis (FEA), Innovation, Innovative Thinking, Leadership Mentoring, Manufacturing Operations, Pharmaceutical Process Development, Prioritization, Process Characterization, Professional Collaboration, Professional Networking, Protein Expression, Publishing, Quality by Design, Regulatory Filings, Strategic Initiative {+ 2 more}
Preferred Skills:
Current Employees apply HERE
Current Contingent Workers apply HERE
US and Puerto Rico Residents Only:
Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.
As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics. As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:
EEOC Know Your Rights
EEOC GINA Supplement
We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another's thinking and approach problems collectively.
Learn more about your rights, including under California, Colorado and other US State Acts
The salary range for this role is
$173,200.00 - $272,600.00
This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee's position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.
The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.
We offer a comprehensive package of benefits. Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits.
You can apply for this role through https://jobs.merck.com/us/en (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.
San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance
Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles' Fair Chance Initiative for Hiring Ordinance
Search Firm Representatives Please Read Carefully
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company. No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.
Employee Status:
Regular
Relocation:
Domestic
VISA Sponsorship:
Yes
Travel Requirements:
10%
Flexible Work Arrangements:
Not Applicable
Shift:
Not Indicated
Valid Driving License:
No
Hazardous Material(s):
n/a
Job Posting End Date:
06/26/2026
*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.

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