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.