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Downstream Process Jobs in Upton, MA (NOW HIRING)

Managed Staffing

Purification Scientist

Boston, MA · On-site

$44 - $46/hr

Monday-Friday | 8:00 AM-5:00 PM (40 hrs/week Position Summary Seeking an early-career Biologist / Purification Scientist to join the Downstream Process Development team in Boston, MA. This role will ...

AT Process Technologies

Process Chemist

Waltham, MA · On-site

$130K - $200K/yr

Develop and optimize core synthesis and downstream processing, evaluating competing technical pathways and justifying key decisions using experimental results, process modeling, cost, and scale-up ...

Sartorius AG

Process Technology Engineer

Marlborough, MA · On-site

$95K - $120K/yr

Join Sartorius as a Process Technology Engineer, supporting upstream and downstream bioprocess solutions across the full project lifecycle-from customer discovery through project execution. You will ...

Repligen Corporation

Scientist II

Waltham, MA · On-site

• The Scientist II, Downstream Processing will independently design, execute, and interpret studies to test and characterize new and prototype downstream processing technologies, equipment, and ...

Merck & Co.

Scientist II

Waltham, MA · On-site

$113.60 - $163.30/hr

The Scientist II, Downstream Processing will independently design, execute, and interpret studies to test and characterize new and prototype downstream processing technologies, equipment, and ...

New

RepliGen Corporation

Scientist II

Waltham, MA · On-site

$113.60 - $163.30/hr

The Scientist II, Downstream Processing will independently design, execute, and interpret studies to test and characterize new and prototype downstream processing technologies, equipment, and ...

Repligen

Scientist II

Waltham, MA · On-site

The Scientist II, Downstream Processing will independently design, execute, and interpret studies to test and characterize new and prototype downstream processing technologies, equipment, and ...

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Downstream Process information

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How much do downstream process jobs pay per hour?

As of Aug 21, 2026, the average hourly pay for downstream process in Upton, MA is $26.82, according to ZipRecruiter salary data. Most workers in this role earn between $21.44 and $30.58 per hour, depending on experience, location, and employer.

What is a downstream process?

A Downstream Process refers to the series of steps involved in the purification and recovery of biological products, such as proteins, enzymes, or antibodies, after they have been produced by microorganisms or cells during fermentation or cell culture. It typically includes cell separation, product isolation, purification, and polishing to achieve the desired product quality and purity. Downstream processing is crucial for ensuring that biopharmaceutical products meet regulatory and safety standards before they reach the market.

What are the key skills and qualifications needed to thrive as a downstream process engineer?

To thrive as a Downstream Process Engineer, you need a solid background in chemical or biochemical engineering, knowledge of purification techniques, and typically a relevant degree. Familiarity with process control systems, chromatography, filtration technologies, and GMP compliance, as well as certifications like Six Sigma, are commonly required. Strong problem-solving, teamwork, and communication skills help you excel in cross-functional teams and address complex production challenges. These skills ensure efficient, high-quality product recovery and compliance with industry standards in biomanufacturing environments.

What are some common challenges faced by professionals working in downstream process roles?

Professionals in downstream process roles often encounter challenges such as optimizing purification steps to maximize yield and product purity while minimizing costs and processing time. They must also troubleshoot issues related to equipment performance, scalability, and regulatory compliance, especially when transitioning from lab-scale to large-scale production. Collaboration with upstream teams, quality assurance, and engineering is critical to address these challenges and ensure a smooth workflow. Staying current with technological advances and regulatory requirements also plays a significant role in day-to-day success.

What is the difference between Downstream Process vs Upstream Process?

AspectDownstream ProcessUpstream Process
PurposePurifies and isolates the target product from the mixtureProduces the initial product, such as cell culture or fermentation
ActivitiesFiltration, chromatography, centrifugation, purificationCell growth, fermentation, media preparation
Work EnvironmentLaboratories, bioprocessing facilitiesBioreactors, fermentation tanks, labs
Required SkillsBioprocessing techniques, chromatography, filtrationMicrobiology, cell culture, fermentation technology

Downstream Process focuses on purifying the product, while Upstream Process involves producing the raw material. Both are essential steps in biopharmaceutical manufacturing, often working sequentially to ensure high-quality product output.

What cities near Upton, MA are hiring for Downstream Process jobs?

Cities near Upton, MA with the most Downstream Process job openings:

Downstream Process jobs near you
Infographic showing various Downstream Process job openings in Upton, MA as of August 2026, with employment types broken down into 1% As Needed, 75% Full Time, 17% Part Time, 1% Temporary, 5% Contract, and 1% Nights. Highlights an 91% Physical, 3% Hybrid, and 6% Remote job distribution, with an average salary of $55,795 per year, or $26.8 per hour.

Advisor, Downstream Process Development - Viral Vectors

Eli Lilly and Company

Boston, MA • On-site

Full-time

Medical, Dental, Vision, Life, Retirement, PTO

Re-posted 11 days ago

Eli Lilly and Company rating

8.8

Company rating: 8.8 out of 10

Based on 63 frontline employees who took The Breakroom Quiz

11th of 86 rated pharmaceutical

Job description

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work-but it's work worth doing. If you're driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.
The Downstream Process Development team is seeking a highly motivated scientist to drive innovation in viral vector purification. The successful candidate will lead platform development to advance DSP capabilities for recombinant adeno-associated virus (AAV) gene therapy products, supporting programs from early development through GMP manufacturing and regulatory submission; collaborating with Analytical Development, CMC Regulatory, and MFG to deliver robust, scalable and efficient manufacturing processes.
Key Responsibilities
  • Design and execute downstream process development experiments for AAV purification, including affinity capture, ion-exchange chromatography, ultrafiltration/diafiltration, viral filtration, and ultracentrifugation
  • Develop and implement novel AAV purification strategies; establish DSP operating principles and process understanding across diverse serotypes.
  • Develop and apply mechanistic chromatography models to predict column performance, guide operating condition selection, and accelerate scale-up decisions, enabling rapid initiation of new gene therapy programs.
  • Collaborate cross-functionally with upstream process development, analytical development, manufacturing, and quality teams to ensure seamless technology transfer and successful clinical manufacturing.
  • Present experimental findings at internal team meetings, cross-functional reviews, and external conferences; contribute to scientific publications and patent applications as appropriate.
  • Author and review technical documents including process descriptions, batch records, process characterization reports, and CMC sections of IND/BLA filings.
  • Mentor junior scientists, encouraging a culture of scientific excellence and continuous improvement.

Basic Qualifications
  • Ph.D. in Chemical Engineering, Biochemical Engineering, Bioengineering, or a related scientific discipline with 2+ years of relevant experience in downstream process development for biologics or gene therapy products, OR M.S. in Chemical Engineering, Biochemical Engineering, Bioengineering, or a related scientific discipline with 10+ years of relevant industry experience
  • Extensive hands-on experience with various protein purification techniques: chromatography (affinity, ion exchange, HIC) and membrane-based separations (UF/DF, depth filtration).
  • Proficiency in statistical design of experiments (JMP, Minitab) and data analysis.

Preferred Qualifications
  • Experience with recombinant AAV or other viral vector purification (lentivirus, adenovirus).
  • Experience with automation platforms for HTP process screening
  • Proficiency in Python and/or MATLAB for data analysis, model implementation, and automation scripting
  • Knowledge of machine learning / multivariate analysis applied to bioprocess data
  • Strong understanding of viral vector biology, expression systems, and analytical methods used for viral vector characterization.
  • Excellent problem-solving skills, critical thinking, and ability to work independently and as part of a team.
  • Strong written and verbal communication skills with the ability to effectively present complex scientific information.
  • Adaptability in a fast-paced environment

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.
Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.
Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women's Initiative for Leading at Lilly (WILL).
Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is
$138,000 - $202,400
Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly's compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.
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About Eli Lilly

Sourced by ZipRecruiter

Eli Lilly, based in Indianapolis, IN, US, is one of the pioneers in the pharmaceutical industry with a rich history dating back to 1876. This global pharmaceutical company focuses on discovering, developing, manufacturing and selling pharmaceutical products in approximately 120 countries. The company's product categories include endocrinology, oncology, cardiovascular, neuroscience, and immunology. Having invested over $9 billion in research and development in the past decade, Eli Lilly is also committed to creating high-quality medicines that meet real needs. As a recipient of several awards and recognitions, Eli Lilly is known for its focus on life-saving research and drug development. Their mission is to make medicines that help people live longer, healthier, and more active lives.

Industry

Pharmaceutical product wholesalers

Company size

10,000+ Employees

Headquarters location

Indianapolis, IN, US

Year founded

1876

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