Associate Director of Enterprise Systems

The Associate Director of Enterprise Systems serves as the enterprise system and process owner for a portfolio of mission‑critical Enterprise Systems within a GxP‑regulated Contract Development and Manufacturing Organization (CDMO). This role has end‑to‑end accountability for the strategy, governance, delivery, and lifecycle management of multiple enterprise platforms, including but not limited to:

• ERP (e.g., SAP ByDesign, S/4HANA, Microsoft Dynamics, Oracle NetSuite)
• CMMS (e.g., Blue Mountain)
• VMS (e.g., Kneat)
• MES  (e.g. Rockwell PharmaSuite, Apprentice, Tulip)
• Other regulated enterprise systems supporting Manufacturing, Quality, Engineering, Supply Chain, and Finance

The Associate Director of Enterprise Systems ensures these systems collectively enable compliant, scalable, and efficient operations, while maintaining data integrity, system validation, and alignment with business strategy and regulatory expectations.

This leader oversees a cross‑functional applications team, acts as a primary liaison between business stakeholders, IT leadership, and external partners, and drives standardization, integration, and continuous improvement across the enterprise application landscape.

Essential Job Functions

Enterprise Systems Ownership & Strategy

• Serve as the overall enterprise owner and single point of accountability for the organization’s Enterprise Systems portfolio, including ERP, CMMS, VMS, MES, and other regulated systems.
• Define and maintain application governance frameworks including change control, access management, system ownership, periodic reviews, and lifecycle management in alignment with 21 CFR Part 11, GAMP 5, and EU Annex 11.
• Establish and enforce standards for data integrity, master data management, configuration management, and system documentation across all enterprise platforms.
• Own and maintain a multi‑year Enterprise Systems roadmap, ensuring alignment with organizational growth, manufacturing strategy, regulatory requirements, and IT objectives.
• This role does not include ownership of the Quality Management System (QMS, Veeva Vault) or QC Laboratory Systems, which are managed under separate functional ownership outside of IT Enterprise Systems.

Implementation & Program Leadership

• Lead and oversee enterprise application implementations and major enhancements, including ERP, CMMS, VMS, and MES initiatives.
• Direct project planning, resource allocation, milestone tracking, risk management, and executive reporting across multiple concurrent application programs.
• Partner with functional leaders across Manufacturing, Quality, Engineering, Supply Chain, Finance, Technical Services, and Warehouse Operations to define business requirements, system designs, and acceptance criteria.
• Manage relationships with system integrators, software vendors, and third‑party service providers, ensuring delivery quality, regulatory compliance, and adherence to scope and timelines.
• Oversee Computer System Assurance (CSA) and Computer System Validation (CSV) activities for all regulated Enterprise Systems, ensuring compliant implementation, documentation, and ongoing validated state.

Integration & Architecture Oversight

• Own key decisions related to enterprise application architecture, integrations, data flows, and security models.
• Coordinate design, testing, and support of integrations between ERP, MES, CMMS, VMS, LIMS, WMS, and other connected systems.
• Ensure Enterprise Systems operate as a cohesive, integrated ecosystem supporting end‑to‑end business processes.

Business Process Ownership

• Act as process owner or co‑owner for core enterprise business processes spanning:
• Finance and Controlling
• Supply Chain and Procurement
• Manufacturing and MES execution
• Asset Management and Maintenance (CMMS)
• Validation and Quality documentation (VMS)
• Drive process standardization, optimization, and automation across systems.
• Ensure processes are documented, controlled, and continuously improved post‑go‑live.
• Partner with Quality and Regulatory Affairs to ensure system-supported processes remain inspection-ready and compliant with applicable regulations.

Team Leadership & Development

• Build, lead, and develop a high-performing enterprise systems team, including business analysts, systems analysts, project managers, and technical writers aligned to the systems portfolio.
• Establish clear goals, performance expectations, and development plans aligned with organizational values and IT strategy.
• Foster a culture of accountability, collaboration, and continuous improvement.
• Identify skills gaps and address them through hiring, coaching, training, and vendor partnerships.

Stakeholder Engagement & Change Management

• Serve as a trusted partner to executive leadership, business process owners, and functional leaders.
• Translate complex business needs into scalable, compliant application solutions.
• Lead organizational change management efforts for Enterprise Systems, including communication plans, training strategies, and user adoption programs.
• Provide regular status updates, risk assessments, and roadmap reviews to IT leadership and executive sponsors.
• Champion process standardization and enterprise systems adoption across all functional areas of the business.

Operations & Continuous Improvement

• Oversee day‑to‑day operations of Enterprise Systems, including incident management, enhancements, periodic reviews, and vendor support.
• Develop and monitor KPIs and SLAs related to system availability, process efficiency, compliance, and business value realization.
• Identify and lead continuous improvement initiatives leveraging enterprise application capabilities.
• Maintain awareness of product releases, regulatory expectations, and industry best practices relevant to pharmaceutical manufacturing and CDMO operations.

Special Job Requirements

• Bachelor’s degree in Information Technology, Computer Science, Business Administration, Engineering, or a related field.
• 12-15+ years of progressive experience managing Enterprise Systems, with leadership experience across multiple platforms (ERP, MES, CMMS, VMS, etc.).
• Demonstrated experience leading large‑scale enterprise system implementations in regulated environments.
• Strong understanding of GxP compliance, including FDA 21 CFR Part 11, GAMP 5, and EU Annex 11.
• Proven ability to lead cross‑functional teams and manage complex, multi‑workstream programs.
• Excellent communication skills with the ability to engage both technical and non‑technical stakeholders.

Additional Preferences

• Experience with SAP S/4HANA, Blue Mountain BMRAM, Kneat VMS, and/or commercial MES platforms.
• Strong background in system integrations, data governance, and reporting/analytics.
• Familiarity with Jira or similar project and service management tools.
• Experience in pharmaceutical, biotech, medical device, or CDMO manufacturing environments.
• Master’s degree, MBA, or relevant certifications (SAP, PMP, etc.) a plus.

Additional info about INCOG BioPharma Services: 

At INCOG BioPharma we have built a world-class CDMO for parenteral injectable drugs. Our culture and priorities are different by design: focused on building long-term value for our customers, we are committed to a service-culture mindset, technical excellence, and a collaborative and team-centered approach to doing business.  

If you crave the challenge of creating systems from scratch and believe you have insights for a better way of doing business, which benefits customers by ensuring quality outcomes and accelerating their route to market, we want to hear from you. Unless otherwise specified, all positions are based out of our Fishers, IN offices. Please note, we are a smoke-free campus. 

INCOG BioPharma is an Equal Opportunity Employer and prohibits discrimination and harassment of any kind.  All employment decisions at INCOG BioPharma are based on business needs, job requirements and individual qualifications, without regard to race, color, religion or belief, sex (including pregnancy), age, physical disability, sexual orientation, family or parental status, or any other status protected by the laws or regulations in the locations where we operate. We will not tolerate discrimination or harassment based on any of these characteristics. 

Qualified applicants must be authorized to work in the United States on a full-time basis. INCOG 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. 

By submitting your resume and details, you are declaring that the information is correct and accurate.