MES Engineer - Lilly Medicine Foundry

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We're looking for people who are determined to make life better for people around the world.

Lilly's Purpose

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We're looking for people who are determined to make life better for people around the world.

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.

What You'll Be Doing:


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. This role sits at the intersection of systems configuration, GxP compliance, and operational collaboration requiring someone who can drive alignment across engineering, operations, and quality stakeholders.

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.
• Coordinating with the MES vendor on area-specific requirements, issue resolution, and deliverable review.
• Facilitating user acceptance testing (UAT) and supporting end-user training and go-live readiness activities for your area.
• Communicating status, risks, and issues to the MES Project Manager and broader leadership in a clear and timely manner.

How You Will Succeed:

• Bring 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.
• Serve as the primary MES technical contact for your area, translating requirements into functional MES workflows in collaboration with process engineering and operations.
• Anticipate configuration challenges within your modality scope, escalate risks proactively, and work with the broader implementation team and to drive timely resolution.
• Build a working understanding of the Foundry manufacturing processes, unit operations, and quality expectations, applying that knowledge directly to MES configuration and validation decisions.
• Ensure all MES configurations and data flows adhere to data integrity principles, 21 CFR Part 11, and Lilly cybersecurity requirements.
• Apply strong analytical and problem-solving skills to troubleshoot MES configuration issues, triage defects during testing, and support root cause analysis during and after go-live.
• Communicate effectively with both technical colleagues and non-technical manufacturing stakeholders; translate MES capabilities and constraints into terms operators and quality staff can act on.
• Champion end-user adoption, supporting training, change management, and on-the-floor go-live assistance in coordination with the broader MES project team.
• Review and approve documentation related to areas of responsibility (Validation Lifecycle documents, executed IQPQ protocols, etc.) as appropriate.
• Stay active and current in business technology trends, direction and innovation related to business process and technology areas of focus by participating in external forums, conferences, and other venues as necessary.

What You Should Bring

• Hands-on experience configuring and implementing a commercial MES platform (Apprentice Tempo, Rockwell Pharma Suite, Emerson Syncade, Siemens Opcenter, or equivalent) in a GMP pharmaceutical manufacturing environment.
• Demonstrated ability to 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.
• Ability to 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.

Your Basic 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, 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.

Other Information:

• Initial location will be based out of Indianapolis, Indiana.
• Permanent location will be at the new Lilly Medicines Foundry in Lebanon, Indiana.

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 Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women's Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.

Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is
$126,000 - $224,400

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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