Principal Scientist GMP Environmental Monitoring Lilly Medicine Foundry

Lilly recently announced a $4.5 billion investment to create the Lilly Medicine Foundry — the first-ever facility to combine research and manufacturing in a single location, expanding capacity for clinical trial medicines while reducing costs and environmental impact. 

Analytical GMP Laboratories (AGL) supports GMP testing across the Lilly Medicine Foundry (LMF) and the broader Product Research & Development (PRD) network, spanning environmental monitoring, microbiology, GMP testing, raw materials, and cleaning/investigations. AGL sits at the intersection of science and quality — this role offers the opportunity to shape the analytical compliance program from the ground up and help drive quality culture at a cutting-edge facility. 

About the Role 

The Principal Scientist, GMP EM serves as the technical owner for cleanroom EM and utility monitoring programs supporting GMP manufacturing operations within the Medicine Foundry Analytical GMP Laboratory. This role oversees daily EM team operations, ensures timely and compliant monitoring execution across classified manufacturing areas, and supports contamination control and production readiness. The Principal Scientist provides technical guidance, develops EM technicians and analysts, serves as the primary escalation point for cleanroom and environmental excursions, and partners with Manufacturing, QC, Facilities, and Quality Assurance to maintain inspection readiness. The role also leads and supports root cause investigations and ensures adherence to cGMP, ALCOA+, and applicable quality and regulatory requirements. 

What You'll Do 

• Own the Cleanroom EM Program: Serve as the site's technical SME for cleanroom and utility monitoring programs — shaping sampling strategy, risk assessments, alert/action limits, and alignment with the site's contamination control strategy from the ground up. 

• Be a Visible Partner on the Manufacturing Floor: Coordinate shift-based EM activities in classified production areas, support manufacturing operations directly, and respond in real time to production needs and environmental concerns. 

• Drive Readiness for a First-of-Its-Kind Facility: Support EMPQs, cleanroom qualifications, utility monitoring readiness, and validation activities that get manufacturing started — and keep it running at GMP standard. 

• Ensure Data Integrity Across Systems: Review and approve EM and lab records, SOPs, and controlled documents, keeping data accurate and audit-ready in systems like MODA and LabVantage. 

• Keep Equipment and Methods Inspection-Ready: Own instrument qualification, calibration, maintenance, and method readiness so testing never misses a beat. 

• Lead Investigations That Matter: Drive root cause investigations for environmental excursions and manufacturing deviations, partnering across Manufacturing, QA, QC, and Facilities to close CAPAs on time. 

• Champion Inspection Readiness: Keep practices and data aligned with cGMP, FDA, EMA, EU GMP Annex 1, USP <1116>, ISO 14644, and 21 CFR 210/211 — and be the one who confidently presents EM data during regulatory inspections. 

• Build the Team: Train, mentor, and develop EM analysts and technicians, instilling aseptic best practices and a "Right First Time" quality culture. 

• Optimize How the Work Gets Done: Plan staffing and resources to meet production schedules, manage budget, and drive continuous improvement in efficiency and cost. 

• Lead by Example on Safety: Ensure all lab, cleanroom, and manufacturing support work is performed safely and in full GMP compliance. 

Minimum Qualifications 

• BS or MS in Microbiology, Biology, Biochemistry, Pharmaceutical Sciences, or a related life science field. 

• 5+ years experience in GMP pharmaceutical microbiology or EM experience including experience interacting with regulatory agencies. 

• Qualified 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 Skills and Preferences 

• Experience with aseptic manufacturing or sterile drug product operations (fill–finish, lyophilization). 

• Proficiency with EM data systems including MODA, LabVantage, Metasys, and quality management systems (TrackWise, Veeva Vault). 

• Hands-on experience with EM sampling instruments: Met One, Climent, Air Ideal, MAS 100, Gas Sampling equipment, Lighthouse, and PMS systems. 

• Working knowledge of microbial identification techniques (MALDI-TOF, Vitek, Gram stain) and bioburden/endotoxin testing. 

• Experience assisting with the development of qualification curricula and on-the-job training plans. 

• Experience working in a greenfield or start-up GMP environment, including contributing to cleanroom qualification, SOP authoring from scratch, equipment selection and qualification, and establishing a quality culture from the ground up 

Additional Information 

• Location: Initial location at Parkwood West, Carmel, IN, with occasional work at Lilly Technology Center, Indianapolis. Permanent location at the Lilly Medicine Foundry in Lebanon, IN. 

• Travel: Less than 5% domestic 

• Regular work in controlled cleanroom environments (ISO 5–8 / Grade A–D) requiring gowning per applicable SOP requirements. 

• May require occasional off-hours, weekend, or on-call availability to support critical manufacturing campaigns or investigation response. 

• Physical requirements include standing for extended periods, walking throughout the facility, and performing gowning activities.