MES Engineer

Eli Lilly and Company

MES Engineer at Lilly Medicine Foundry responsible for MES implementation and configuration. Collaborating with engineering, operations, and quality to optimize manufacturing processes.

Posted 5/19/2026full-timeIndianapolis • 🇺🇸 United StatesMid-LevelSenior💰 $126,000 - $224,400 per yearWebsite

About the role

Key responsibilities & impact

As an MES Engineer at the Lilly Medicine Foundry, you will serve as both a hands-on technical practitioner and the functional lead for a manufacturing modality area for a SaaS-based MES implementation.
Key responsibilities include: Serving as the MES area lead for a manufacturing modality (e.g., small molecules, peptides, biologics), owning end-to-end configuration and delivery.
Configuring, building, and testing MES workflows, electronic batch records (eBRs), and digital work instructions aligned to manufacturing process requirements.
Partnering with process engineers, operations, and to translate manufacturing procedures into MES-executable digital workflows.
Supporting IQ/OQ/PQ validation activities, authoring and reviewing validation lifecycle documents, and ensuring compliance with 21 CFR Part 11, GAMP 5, and Lilly CSV/CSA standards.
Communicating status, risks, and issues to the MES Project Manager and broader leadership in a clear and timely manner.

Requirements

What you’ll need

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, Werum PAS-X)
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.
Hands-on experience configuring and deploying MES platforms in a pharmaceutical GMP environment, ideally including recipe management, eBR authoring, and electronic workflow design.
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.
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.

Benefits

Comp & perks

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
well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)

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Hard Skills & Tools

MES configurationeBR authoringdigital workflow designComputer System Validation (CSV)GMP compliancerecipe managementbatch executionmaterial trackingequipment managementUser Requirements Specifications (URS)

Soft Skills

communicationleadershipcollaborationproblem-solvingorganizational skills