Principal Engineer, Downstream Processing

Job ID: R-110897Company: LillyLocation: Boston, Massachusetts, United States of AmericaJob Type: Full TimeCategory: EngineeringPosted Date: 2026-09-08At 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. Job SummaryTo support our growing genetic medicines pipeline, we are seeking to expand expertise of our research-grade pilot manufacturing team at Lilly's Harborside location in Boston, MA.The Principal Engineer, Downstream Processing will provide direct support for the tech transfer of small-scale purification conditions to manufacturing scale (e.g., 250L-derived downstream train). This role will provide expertise required for downstream analyses — including yield and recovery calculations across unit operations, chromatogram interpretation (e.g., peak shape, resolution, area under the curve), filtration performance metrics (e.g., flux decay, TMP trends, membrane fouling indicators) and overall root cause troubleshooting within and between unit operations. This role will be integral in defining the laboratory's downstream technical agenda. The successful applicant will have deep technical expertise in their areas of responsibility and demonstrate strong data-driven problem-solving capabilities.Key ResponsibilitiesPossess in-depth knowledge and demonstrated technical capability with downstream unit operations including depth filtration, multiple chromatography modes (e.g., affinity, ion exchange, hydrophobic interaction), ultracentrifugation, and tangential flow filtration (TFF).Collaborate with early and late-phase development organizations to ensure well-understood and robust processes are transferred.Maintain accurate records and interpret data to provide detailed information and analyses.Troubleshoot issues as they occur and identify trends and opportunities to reduce process variability and improve product recovery and quality.Create and review documents including laboratory SOPs, material specifications, protocols, and work instructions.Flexibility to accept new projects, prioritizations, and challenges.Basic RequirementsBS degree in biology, chemistry, biochemistry, chemical engineering, or similar discipline with at least 5 years of relevant experience in downstream scale-up/scale-down process development.MS degree in biology, chemistry, biochemistry, chemical engineering, or similar discipline with at least 3 years of relevant experience in downstream scale-up/scale-down process development.PhD will not be considered at this job levelQualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1.Additional PreferencesDirect experience with purification of recombinant AAV and/or lentivirus.Hands-on experience with mammalian and/or insect cell derived feed streams.Exposure to process automation and single-use technologies.Working knowledge of Unicorn software.Proficiency in Microsoft Office and statistical analysis software (e.g., JMP).Detail-oriented, self-motivated, and excited to take on new challenges.Demonstrated strong interpersonal skills.Demonstrated strong verbal and written communication skills.Demonstrated ability to participate in and facilitate decision-making.Work EnvironmentLimited occasional evening or weekend work required.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 () 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 (View email address on click.appcast.io), 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$112,500 - $165,000Full-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.#WeAreLillySkillsdownstream unit operationsfiltration performance metricschromatography modesroot cause troubleshootingyield and recovery calculationschromatogram interpretationprocess automationsingle-use technologiesunicorn softwarestatistical analysis softwarelaboratory sopsmaterial specificationsprotocol developmentwork instructionsprocess scale-upprocess scale-downrecombinant aav purificationlentivirus purificationmammalian cell feed streamsinsect cell feed streamsdecision-making facilitationinterpersonal skillsverbal and written communication