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Bioprocess Engineer Jobs (NOW HIRING)

Whether your background is in bioprocess engineering, synthetic biology, automation, operations, manufacturing, business development, or something unexpected, please reach out. Who We're Looking For

Whether your background is in bioprocess engineering, synthetic biology, automation, operations, manufacturing, business development, or something unexpected, please reach out. Who We're Looking For

Your Role: We're seeking a Bioprocess Applications Engineer 3 to join the Single Use and Integrated Systems Product Development team, part of MilliporeSigma's Process Solutions business unit. Based ...

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Bioprocess Engineering, Bioprocesses, Biotechnology, Cell Physiology, Centrifugation, Chemical Engineering, Chromatographic Techniques, Chromatography, Column Chromatography, Data Analysis ...

Education * BS degree or higher in Microbiology, Molecular Biology, Bioprocess Engineering, Food Safety, or a related scientific discipline. * Advanced degree (MS or PhD) preferred. Experience * With ...

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Bioprocess Engineer information

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$11K

$83K

$113.5K

How much do bioprocess engineer jobs pay per year?

As of Jul 25, 2026, the average yearly pay for bioprocess engineer in the United States is $82,999.00, according to ZipRecruiter salary data. Most workers in this role earn between $50,000.00 and $102,500.00 per year, depending on experience, location, and employer.

What Is Bioprocess Engineering?

A bioprocess engineer uses biological materials to create a variety of products. As a bioprocess engineer, you apply your biology and chemistry skills to create foods, products used in the agriculture industry, biofuels, pharmaceuticals, and water filtration systems, among other products. Qualifications for this career depend on the specific duties of a job, but you should obtain at least a bachelor’s degree in biology or chemistry. Most bioprocess engineers go on to pursue a graduate degree as well. You also need experience in a laboratory setting. The biotechnology field is growing quickly, so an entry-level engineer job in the field is perfect for those looking to pursue this a career in this industry.

What is the difference between Bioprocess Engineer vs Process Development Scientist?

AspectBioprocess EngineerProcess Development Scientist
Required CredentialsBachelor's or Master's in Bioengineering, Biotechnology, or related fieldsBachelor's or Master's in Bioengineering, Biotechnology, or related fields
Work EnvironmentManufacturing facilities, production lines, biotech companiesResearch labs, R&D departments, biotech firms
Employer & Industry UsageBiotech, pharmaceutical manufacturing, contract manufacturing organizationsBiotech, pharmaceutical R&D, research institutions
Common Search & ComparisonYesYes

While both roles require similar educational backgrounds and work in biotech environments, Bioprocess Engineers focus on scaling up and optimizing manufacturing processes, whereas Process Development Scientists concentrate on developing and refining processes during early research stages. Understanding these differences helps professionals choose the right career path or job search focus.

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

To thrive as a Bioprocess Engineer, you need a strong background in chemical or biochemical engineering, with expertise in cell culture, fermentation, and process optimization, usually backed by a relevant engineering degree. Familiarity with bioprocess simulation software, laboratory automation tools, and regulatory standards like GMP is critical. Strong problem-solving abilities, attention to detail, and effective teamwork are standout soft skills for this role. These competencies ensure efficient development and scaling of bioprocesses, compliance with quality standards, and successful collaboration in biomanufacturing environments.

What are some common challenges faced by Bioprocess Engineers when scaling up production from the lab to industrial levels?

Bioprocess Engineers often encounter challenges when scaling up processes, such as maintaining product quality and consistency, optimizing yield, and ensuring efficient mixing and mass transfer in larger bioreactors. Unexpected issues like contamination risks and differences in process dynamics can arise at larger scales, requiring close collaboration with quality assurance, manufacturing, and R&D teams. Successful scale-up demands strong problem-solving skills, adaptability, and a thorough understanding of both biological and engineering principles.

What does a Bioprocess Engineer do?

A Bioprocess Engineer designs and optimizes processes that use living cells or their components, such as bacteria or enzymes, to produce products like pharmaceuticals, biofuels, and food ingredients. Their work involves scaling up laboratory processes to industrial production, ensuring efficiency, safety, and regulatory compliance. They collaborate with scientists, production teams, and quality assurance to troubleshoot issues and improve yields. Bioprocess Engineers play a critical role in the biotechnology and pharmaceutical industries by bridging the gap between research and manufacturing.
What cities are hiring for Bioprocess Engineer jobs? Cities with the most Bioprocess Engineer job openings:
What are the most commonly searched types of Bioprocess Engineer jobs? The most popular types of Bioprocess Engineer jobs are:
Who are the top companies hiring for Bioprocess Engineer jobs? The top employers for Bioprocess Engineer jobs are:
What states have the most Bioprocess Engineer jobs? States with the most job openings for Bioprocess Engineer jobs include:
Infographic showing various Bioprocess Engineer job openings in the United States as of July 2026, with employment types broken down into 31% Internship, 17% As Needed, 46% Full Time, 1% Part Time, 4% Contract, and 1% Summer. Highlights an 93% Physical, 2% Hybrid, and 5% Remote job distribution, with an average salary of $82,999 per year, or $39.9 per hour.
Senior Scientist I/II, Bioprocess Development

Senior Scientist I/II, Bioprocess Development

Flagship Pioneering, Inc.

Cambridge, MA

$100K - $136K/yr

Other

Medical, Retirement

Posted 7 days ago


Job description

COMPANY DESCRIPTION 

Flagship Pioneering is a bioplatform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies.   

What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet.   

Many of the companies Flagship has founded have addressed humanity's most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE's "Change the World" list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company's annual list of the World's Most Innovative Companies. 

THE ROLE

We are seeking a Senior Scientist I/II, bioprocess development and microbial production subject matter expert and in-lab technical lead for a high impact, novel biological platform. This role will focus primarily on fermentation process development, translating early-stage biological systems into scalable and manufacturable processes. The successful candidate will work collaboratively at the interface between microbial engineering and bioprocess optimization.

KEY RESPONSIBILITIES

  • Design, execute, and iterate on bioprocess experiments to support scalable fermentation process development including collaboration with Strain Development on strain improvements to support bioprocess productivity and robustness, media development, feeding design, mass transfer optimization, and process control
  • Translate biological discoveries into robust production systems by improving yield, productivity, and process reproducibility
  • Contribute to implementation and buildout of experimental frameworks for systematic process improvement, including DOE-based optimization and fermentation analytics
  • Execute technology transfer to external CROs, CMOs, or manufacturing partners as subject matter expert as needed

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

  • PhD in biochemical engineering, microbiology, chemical engineering, or a related discipline
    • Scientist I: At least 5-7 years of professional experience, including 1+ years hands-on developing microbial fermentation processes in an industrial or translational setting
    • Scientist II: At least 8-11 years of professional experience, including 3+ years hands-on developing microbial fermentation processes in an industrial or translational setting
  • Demonstrated expertise in fermentation process development & scale-up, including optimizing parameters such as oxygen transfer, feeding regimes, media composition, etc.
  • Experience optimizing high-cell-density microbial fermentations
  • Hands-on experience developing and optimizing microbial fermentation across scales (e.g., 250 mL bench reactors through 50 L pilot-scale systems)
  • Experience designing and executing fermentation experiments using systematic optimization approaches, such as DOE or structured process screening

PREFERRED EXPERIENCE

  • Experience working with external partners (CROs, CMOs, or manufacturing facilities) to develop or transfer fermentation processes, including preparation of process documentation and technical oversight
  • Experience developing fed-batch fermentation processes across a range of industrial microbial hosts, including bacteria, yeast, and filamentous fungi
  • Experience improving production performance through close collaboration or co-ownership of targeted strain engineering activities

LOCATION:  Cambridge, MA

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity's most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE's "Change the World" list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company's annual list of the World's Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, "FSP") do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering's internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

#LI-TL1

The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protocos's good faith estimate as of the date of publication and may be modified in the future.