Senior Manager, HR Operations and Systems

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health and sustainability exponentially accelerate scientific progress in areas ranging from cancer detection and treatment to nature-positive agriculture.   

 What sets Flagship apart is our ability to advance biotechnology by uniting life science innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet.   

Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. 

Position Overview: 

Flagship Pioneering is seeking a Senior Manager, HR Operations & Systems to own and evolve our HR systems ecosystem, with primary responsibility for UKG and broad oversight of platforms including Greenhouse and other HR technologies. This role will drive day-to-day administration, governance, integrations, and future-state strategy of HR systems to ensure compliance, enable scalable service delivery, strengthen data integrity, and support a seamless employee experience across the lifecycle. Reporting to the Associate Director, HR Operations & Analytics, this leader will partner closely with HR, Legal, Payroll, Finance, and Enterprise Applications / IT to design system-enabled HR operations that are scalable, well-governed, and built for growth. 

Role Summary 

The Senior Manager, HR Operations & Systems will serve as the business owner for Flagship’s HR systems ecosystem within HR Operations, with primary responsibility for the strategy, administration, optimization, and operational enablement of core HR platforms, including UKG, Greenhouse, and other HR technologies across the employee lifecycle. 

Reporting to the Associate Director, HR Operations & Analytics, this role will partner closely with HR Operations, Talent, Total Rewards, Learning & Culture, Legal, Payroll, Finance, People Analytics, and Enterprise Applications / IT to ensure systems support the HR function in a scalable, compliant, and analytically sound way. 

This leader will help stitch together the HR systems landscape through thoughtful integrations, controls, documentation, and future-state HR tech strategy, while acting as a subject matter expert to IT for implementation and technical design. 

Key Responsibilities 

HR Systems Ownership & Administration 

• Serve as the primary HR business owner for HR systems, with deep ownership of UKG and operational oversight of other HR and talent platforms such as Greenhouse, TalentWall, Crosschq, LinkedIn Recruiter, Pequity, and future tools. 

• Manage day-to-day administration of HR systems, including configuration, permissions, security roles, workflows, testing, issue resolution, release support, and operational documentation. 

• Ensure HR systems are structured and maintained to support scalable service delivery, consistent HR operations, and strong user experience across the employee lifecycle. 

• Maintain system standards, field logic, process flows, and governance documentation to improve consistency and reduce operational ambiguity. 

Systems Architecture, Process Design & Integrations 

• Architect HR systems and processes from an operational perspective, ensuring systems support onboarding, transfers, promotions, offboarding, compliance requirements, and service delivery across the employee lifecycle. 

• Design and optimize integrations across the HR systems landscape, including key connections such as UKG-ADP and Greenhouse-UKG, to improve data flow, reduce manual work, and strengthen downstream reporting and controls. 

• Partner with Enterprise Applications / IT to define technical requirements, integration priorities, testing strategy, and implementation needs; serve as the HR SME for system changes and implementations while IT owns technical implementation and vendor management. 

• Be sufficiently hands-on and technically fluent to configure systems directly where appropriate and to effectively guide or direct technical work when builds are completed by IT or other partners. 

• Identify automation opportunities and future-state improvements across HR systems to improve scalability, reduce friction, and support evolving business needs. 

Compliance, Controls & Governance 

• Partner with HR Operations teammates, Legal, and other stakeholders to ensure systems are designed and configured to enable compliance, controls, audit readiness, and consistent execution of HR processes. 

• Manage system-enabled governance, including permissions, process controls, documentation logic, policy acknowledgement workflows, and audit-supporting records. 

• Help ensure systems support compliance execution across key areas such as documentation completeness, training administration, process controls, and employee record quality. 

• Support the creation of scalable, system-enabled HR ways of working by translating process requirements into governed workflows and operational logic. 

Analytics Enablement & Data Integrity 

• Partner closely with the People Analytics Manager to ensure HR systems are structured to support reliable reporting, meaningful analytics, and consistent data definitions. 

• Improve data integrity across systems by aligning field design, ownership, process inputs, and integrations to reduce discrepancies and improve trust in people data. 

• Ensure systems are built with analytics needs in mind, and conversely, help refine systems based on reporting and data-quality insights. 

• Support the broader HR function in strengthening compliance intelligence, scalable service delivery, and experience optimization through better system design and cleaner data. 

Cross-Functional Partnership & Change Enablement 

• Build strong working relationships across HR, IT, Payroll, Finance, Legal, and other G&A partners to align systems strategy and operational delivery with business needs. 

• Support change enablement through documentation, process clarity, and partnership with HR Operations and other HR team members; formal training delivery is not a core responsibility, but this role will help ensure systems and documentation are set up for successful adoption. 

• Contribute to future-state HR tech strategy, including evaluation of system opportunities and support for upcoming initiatives. 

What Success Looks Like 

• HRIS and the broader HR systems landscape are well-governed, well-documented, and operationally effective. 

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