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Downstream Process Engineer Jobs (NOW HIRING)

Agilent

Process Engineer, Downstream

Frederick, CO · On-site

$124K - $194K/yr

Join a growing team with this exciting new opportunity for an expert level Downstream Process Engineer. Work on a dynamic, fast-paced, large capacity oligonucleotide API production facility design ...

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Downstream Process Engineer information

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$49.5K

$92K

$142.5K

How much do downstream process engineer jobs pay per year?

As of Jul 16, 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 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.

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 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.
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What job categories do people searching Downstream Process Engineer jobs look for? The top searched job categories for Downstream Process Engineer jobs are:
Downstream Process Engineer jobs near you
Infographic showing various Downstream Process Engineer job openings in the United States as of July 2026, with employment types broken down into 23% Locum Tenens, 73% Full Time, 1% Part Time, and 3% Contract. Highlights an 85% Physical, 4% Hybrid, and 11% Remote job distribution, with an average salary of $92,018 per year, or $44.2 per hour.

Senior Process Engineer - Downstream (Biologics & Peptides)

Stark Pharma Solutions Inc

Boulder, CO • On-site

$107K - $139K/yr

Contractor

Posted 6 days ago

Job description

Job Title: Senior Process Engineer – Downstream (Biologics & Peptides)

Location: Boulder, CO (100% Onsite)

Duration: 6 Months + Extensions

Start Date: ASAP

Job Summary

We are seeking a Senior Process Engineer with strong expertise in downstream processing to support the development, scale-up, and commercialization of biologics and peptide-based therapeutics. This role will focus on designing, optimizing, and implementing purification processes and manufacturing systems within a GMP-regulated environment.

The ideal candidate will have hands-on experience with chromatography and tangential flow filtration (TFF) technologies, along with a proven track record supporting process scale-up, equipment qualification, and manufacturing startup activities.

Key Responsibilities

  • Lead downstream process development and optimization activities for biologics and peptide products
  • Design, specify, and support implementation of purification systems including chromatography and TFF skids
  • Support process scale-up from development through pilot and commercial manufacturing
  • Drive startup, commissioning, qualification, and troubleshooting of downstream manufacturing equipment
  • Develop and execute process validation and verification strategies aligned with GMP and regulatory requirements
  • Collaborate with MSAT, Upstream, Manufacturing, and Quality teams to ensure process robustness and consistency
  • Author and review technical documentation including process descriptions, validation protocols, and regulatory support documents
  • Serve as a technical SME for downstream purification operations and technologies
  • Mentor junior engineers and support continuous improvement initiatives

Required Qualifications

  • Bachelor’s, Master’s, or PhD in Chemical Engineering, Biochemical Engineering, or related field
  • 8+ years of experience in biopharmaceutical process engineering with strong downstream processing expertise
  • Hands-on experience with:
  • Chromatography systems (affinity, ion exchange, HIC, etc.)
  • Tangential Flow Filtration (TFF) systems
  • Experience supporting equipment startup, commissioning, and qualification activities
  • Strong understanding of process validation and GMP manufacturing environments
  • Experience supporting or leading tech transfer and process scale-up activities
  • Strong troubleshooting, communication, and cross-functional collaboration skills