Principal Scientist Deviation Management Lilly Medicine Foundry

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. 

Lilly recently announced a $4.5 billion investment to create the Lilly Medicine Foundry, a new center for advanced manufacturing and drug development. The first-ever facility of its kind, combining research and manufacturing in a single location, the Medicine Foundry will allow Lilly to further develop innovative solutions to optimize manufacturing processes and increase capacity for clinical trial medicines, while also 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.

The Principal Scientist – Deviation Management leads deviation and out-of-specification (OOS) investigations, root cause analysis, CAPA development, and change control for AGL at the Lilly Medicine Foundry. Reporting to the Senior Advisor and partnering with Manufacturing, Quality Assurance, and Engineering, this role authors clear, defensible investigation reports and CAPA plans, performs hands-on troubleshooting to support investigation conclusions, serves as a quality champion on the Analytical Compliance Excellence (ACE) team, and mentors’ junior investigators.

Key Responsibilities

Deviation Investigation Leadership

• Lead deviation and out-of-specification (OOS) investigations (Minor, Major, Critical), applying structured root cause analysis methods (5-Why, fishbone/Ishikawa, fault tree, Is/Is-Not) to determine true root cause.
• Author and review deviation reports, investigation protocols, and CAPA plans with clear, defensible rationale that meets data integrity (ALCOA+) standards and holds up to regulatory scrutiny.
• Draft CAPA plans that are risk-appropriate, measurable, and linked to verified root causes, and author change control records assessing impact to validated processes, equipment, and systems.
• Perform hands-on troubleshooting and confirmatory testing to distinguish true deviations from analytical or process anomalies; partner with QA, SMEs, and stakeholders from assignment through closure to keep the deviation portfolio on track for right-first-time, on-time completion, and may lead Deviation Review Board meetings.

Quality System & Compliance Excellence

• Serve as a thought leader on the Analytical Compliance Excellence (ACE) team, championing quality priorities across AGL and supporting audit and inspection readiness through clear deviation and CAPA rationale.
• Drive process improvement based on deviation metric analysis, contributing to AGL's continuous improvement roadmap, and support data integrity and training initiatives.

Trend Analysis & Metrics

• Lead cross-functional analysis of investigation trends and deviation metrics, translating data into actionable insights; track deviation, OOS, CAPA, and change control records to closure, escalating at-risk items to leadership.

Mentorship & Capability Building

• Mentor junior investigators and analytical staff on root cause analysis, technical writing, and quality impact evaluation, serving as a go-to resource for GMP compliance and investigation strategy across AGL.

Cross-Functional Collaboration

• Partners with Manufacturing, Quality Assurance, Analytical/QC, Engineering, and AGL branch leads to scope investigations, verify corrective actions, and confirm CAPA effectiveness — engaging the broader PRD network and external labs for cross-site work as needed.
• Collaborate closely with the Senior Advisor on investigation strategy, CAPA prioritization, and change control decisions requiring elevated judgment; may participate in deviation governance teams and other quality initiatives.

Basic Qualifications

• BS in Chemistry, Biochemistry, Engineering, Pharmaceutical Sciences, Biology, or a related scientific/technical discipline.
• BS with 6+ years or MS with 3+ years of progressive GMP manufacturing, quality, or laboratory experience, including direct experience with deviation and OOS investigations, root cause analysis, and CAPA.
• Demonstrated experience authoring investigation protocols, technical reports, and CAPA plans in a regulated environment.
• 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 & Preferences

• Working knowledge of ICH guidelines, FDA regulations (21 CFR Parts 210/211), and cGMP/data integrity (ALCOA+) principles as applied to investigations, CAPA, and change control in a phase-appropriate clinical development environment.
• Experience with electronic quality management systems (e.g., TrackWise, Veeva QMS) and lab informatics/GMP documentation platforms for deviation, CAPA, and change control records.
• Strong root cause analysis skills using structured methodologies (5-Why, fishbone/Ishikawa, fault tree, Is/Is-Not), with the ability to select the right tool for the complexity of the deviation.
• Demonstrated technical writing skills for protocols, investigation reports, and CAPA plans that hold up to regulatory review, paired with hands-on troubleshooting experience on GMP manufacturing equipment or analytical instrumentation.
• Experience drafting and assessing change controls and risk/impact assessments for validated systems, familiarity with Quality Risk Management (QRM) tools (e.g., FMEA), and understanding of lot association within deviations.
• Strong critical thinking and leadership skills — comfortable driving decisions independently, communicating with accountability and intellectual humility, and presenting findings to cross-functional teams and leadership.
• Experience mentoring junior investigators and supporting regulatory inspections (FDA, EMA, or equivalent) or audits related to deviations, CAPA, and change control.

Other Information

• Location: Initial location at Lilly Technology Center, Indianapolis. Permanent location at the new Lilly Medicine Foundry in Lebanon, Indiana.
• Travel: 0 to 10%
• Shift: First shift, 8-hour days/five days per week, with occasional off-shift, weekend, or holiday coverage — including during shutdowns — to support manufacturing demand.
• Physical: Ability to work in a gowned GMP manufacturing and laboratory environment, stand for extended periods, and occasionally handle hazardous materials and solvents while wearing required PPE.

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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

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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