Sr. Principal MES Engineer - Lilly Medicine Foundry

About the role

Lilly is seeking a MES Engineer to join the Lilly Medicine Foundry. The Foundry is a new center for advanced manufacturing and drug development, with a $4.5 billion investment to create a facility combining research and manufacturing in a single location.

Responsibilities

• Serve as the MES area lead for a manufacturing modality (e.g., small molecules, peptides, biologics).
• Owning end-to-end configuration and delivery of MES workflows, eBRs, and digital work instructions aligned to manufacturing process requirements.
• Partner with process engineers, operations, and quality to translate manufacturing procedures into MES-executable digital workflows.
• Support IQ/OQ/PQ validation activities, authoring and reviewing validation lifecycle documents, and ensure compliance with 21 CFR Part 11, GAMP 5, and Lilly CSV/CSA standards.
• Coordinate with the MES vendor on area-specific requirements, issue resolution, and deliverable review.
• Facilitate user acceptance testing (UAT) and support end-user training and go-live readiness activities for your area.
• Communicate status, risks, and issues to the MES Project Manager and broader leadership in a clear and timely manner.

Requirements

• Hands-on experience configuring and deploying MES platforms in a pharmaceutical GMP environment, ideally including recipe management, eBR authoring, and electronic workflow design.
• Lead modality area through all phases of the MES implementation lifecycle — from requirements gathering and configuration through testing, validation, and go-live support.
• Translate manufacturing SOPs, batch records, and process requirements into MES-executable electronic batch records (eBRs), digital work instructions, and recipes.
• Solid understanding of GMP manufacturing concepts, including batch execution, material tracking, equipment management, and electronic records requirements under 21 CFR Part 11.
• Experience participating in or leading Computer System Validation (CSV) activities, including authoring or reviewing User Requirements Specifications (URS), Functional Specifications, and IQ/OQ/PQ protocols under GAMP 5 or equivalent frameworks.
• Identify and communicate technical risks within your area of responsibility, propose mitigations, and escalate appropriately within the project governance structure.
• Experience leading or co-leading a functional workstream within a larger IT or MES implementation project, including coordination of tasks, issue tracking, and stakeholder reporting.
• Working knowledge of pharmaceutical manufacturing operations (e.g., batch manufacturing, material handling, in-process controls) relevant to at least one modality such as small molecules, biologics, peptides, oligonucleotides, or ADCs.
• Excellent communication and collaboration skills; ability to build effective working relationships across manufacturing, engineering, quality, and IT functions in a greenfield environment.
• Strong analytical and problem-solving mindset, with demonstrated ability to work through ambiguity and keep deliverables on track in a fast-paced greenfield program.
• Comfort working in a greenfield startup environment where processes, priorities, and vendor deliverables are evolving; ability to manage multiple concurrent tasks and adapt quickly.
• Strong working knowledge of MES integration concepts, including how MES platforms connect with automation systems, ERP, LIMS, and data infrastructure in a pharmaceutical manufacturing context.

Qualifications

• Bachelor’s degree in Software Engineering, Computer Science, Computer Engineering, or a related field.
• Minimum of 5+ years of experience working with pharmaceutical manufacturing systems or MES platforms (e.g., Apprentice Tempo, Rockwell Automation Pharma Suite, Emerson Syncade, Siemens Opcenter, or equivalent).
• Minimum of 2+ years experience supporting or leading Computer System Validation (CSV) activities in a GMP-regulated environment.
• Experience working within or alongside a pharmaceutical manufacturing operation is required.