Cambridge, MA Contracts Systems Manager

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies 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. Learn more about Flagship  .

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are seeking a Contracts System Manager to serve as the primary owner and administrator of Flagship's Contract Lifecycle Management (CLM) and procurement systems. This individual will be responsible for system configuration, optimization, user support, training, and cross-functional collaboration to ensure the Legal, Procurement, and Finance teams can efficiently manage contracts across Flagship and its portfolio companies. The role requires significant interpersonal engagement—building trusted relationships across business units, influencing stakeholders to adopt new processes, and exercising judgment in navigating competing priorities that require human insight and contextual understanding.

The ideal candidate will have 3–5 years of experience administering CLM platforms (Cobblestone experience strongly preferred), a solid understanding of procurement workflows, and the ability to translate business requirements into technical system configurations. This role requires strong stakeholder engagement skills, attention to detail, and comfort working in a fast‑paced, high‑volume environment.

This is a great opportunity to join a company at the forefront of innovation in technology and science. We are looking for a self‑motivated, entrepreneurial, and kind individual who works hard but doesn't take themselves too seriously. The team you would be joining is tight‑knit and committed to helping one another succeed.

System Administration & Configuration

• Serve as the primary administrator for Flagship's CLM system (Cobblestone), including system configuration, user provisioning, role‑based access control (RBAC), and permissions management
• Design and configure contract workflows, approval routing logic, and dynamic intake forms based on agreement type, spend thresholds, department, or legal requirements—collaborating directly with business owners to understand their operational needs and secure buy‑in on workflow changes
• Manage the company's contract templates, playbook terms, and clause libraries; configure new templates and process workflows as needed
• Maintain repository accuracy, metadata tagging, and taxonomy; identify inefficiencies in current processes and propose workflow design improvements

Integration & Technical Operations

• Oversee and troubleshoot API connections and data syncs between the CLM system and downstream systems (e.g., ERP, procurement platforms, HRIS, e‑signature tools)
• Coordinate with IT on system integrations, security protocols, and technical requirements; serve as a trusted liaison between business functions, IT, and CLM vendor, translating technical constraints into business‑friendly explanations and advocating for user needs in system design decisions
• Test and deploy system updates, patches, and new features from vendors; manage change control to minimize disruption to business users
• Configure and maintain vendor management modules, ensuring seamless data capture and risk assessment during vendor onboarding

User Support & Training

• Provide Tier 1 and Tier 2 support for CLM system users, including day‑to‑day troubleshooting, resolving workflow stalls, and…