Senior Manager, HR Operations and Systems

Flagship Pioneering, Inc.•Cambridge, MA

About The Position

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies that change the world. They unite scientific minds with entrepreneurial company builders and provide capital to enable courageous leaps in human health and sustainability. Flagship has been recognized on FORTUNE’s “Change the World” list and Fast Company’s “World’s Most Innovative Companies” list. The company is seeking a Senior Manager, HR Operations & Systems to own and evolve its HR systems ecosystem, primarily UKG, and oversee platforms like Greenhouse and other HR technologies. This role will manage day-to-day administration, governance, integrations, and future-state strategy of HR systems to ensure compliance, scalable service delivery, data integrity, and a seamless employee experience. The position reports to the Associate Director, HR Operations & Analytics and will partner with HR, Legal, Payroll, Finance, and Enterprise Applications / IT to design scalable, well-governed, and growth-oriented HR operations.

Requirements

Strong hands-on experience with enterprise HRIS administration and configuration; UKG experience strongly preferred, though deep equivalent HRIS experience may be considered.
Experience owning or supporting enterprise HR systems across multiple HR process areas.
Experience designing, managing, or supporting integrations between HRIS, ATS, payroll, and other people systems.
Strong understanding of how systems support employee lifecycle operations, compliance controls, and scalable service delivery.
Experience partnering closely with Enterprise Applications / IT teams on technical requirements, integrations, permissions, and implementation planning.
Strong judgment and ability to manage confidential employee and organizational data responsibly.
Strong written documentation and process-design skills.
Proven track record of independently driving operational improvements and cross-functional initiatives.

Nice To Haves

UKG experience

Responsibilities

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.
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.
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.
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.
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.