Contracts Systems Manager

Flagship Pioneering•Cambridge, MA

9h•Hybrid

About The Position

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

Requirements

Bachelor's degree in Business, Information Systems, Legal Studies, or related discipline
3–5 years of experience as a CLM systems administrator, legal operations specialist, or similar role
Proficiency with contract lifecycle management (CLM) systems and associated workflows; hands-on experience with system configuration, workflow design, and user administration
Understanding of procurement and finance processes, including budgets, payment terms, and vendor engagement
Experience developing and implementing system-driven workflows; comfort with Jira or similar tools for user story creation and tracking
Strong written and verbal communication skills with excellent stakeholder engagement ability, including the capacity to influence without authority, navigate organizational dynamics, and build consensus among diverse business partners
Ability to exercise independent judgment in prioritizing workflow, escalating appropriately, and making nuanced decisions that balance competing stakeholder interests and business objectives
Experience troubleshooting CLM or workflow system issues; ability to promptly identify and solve software and process problems
Detail-oriented with strong organizational and project management skills
Ability to multi-task and work independently in a fast-paced environment; prioritize workflow based on business objectives

Nice To Haves

Experience in biotech, life sciences, pharmaceutical, or regulated industries
Experience configuring or administering Cobblestone CLM system (taxonomy, permissions, template maintenance, workflow configuration)
Familiarity with Coupa or other procurement system integration
Experience with contract intake and legal operations frameworks
Exposure to commercial agreements and legal terms and conditions
Experience leading or actively participating in CLM system implementation projects
Familiarity with FDA regulations, GxP requirements, or clinical contracting in life sciences environments
Proficiency with business applications such as Microsoft 365, Coupa, Cobblestone, DocuSign, and Adobe Acrobat
Ability to work in a scrum/agile environment

Responsibilities

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 addressing error messages
Onboard and train new users (both technical and non-technical) on CLM system functionality and related processes through hands-on coaching, live demonstrations, and personalized support; implement train-the-trainer models and adapt training approaches based on individual learning styles and departmental needs
Develop and maintain CLM training materials, user guides, and Standard Operating Procedures (SOPs); gather user feedback and recommend process improvements
Support onboarding of new Flagship portfolio companies onto established contract standards and CLM processes, serving as a dedicated point of contact who builds rapport with new teams, addresses concerns with empathy, and guides stakeholders through change management during organizational transitions
Cross-Functional Collaboration & Stakeholder Engagement Act as the primary liaison between IT and Finance, Legal, and Procurement teams, translating business processes into technical system requirements
Build and maintain strategic relationships with business colleagues across Flagship and portfolio companies to understand evolving contracting needs, anticipate workflow challenges, and influence adoption of standardized processes through trust, credibility, and demonstrated value
Coordinate directly with external vendors, counterparties, and law firms on contract logistics and system-related clarifications, exercising diplomacy and sound judgment to resolve ambiguities, manage expectations, and maintain productive working relationships
Reporting & Analytics Build dashboards and generate contract metrics to inform Legal leadership and cross-functional stakeholders; analyze trends and provide recommendations to improve contract operations efficiency, presenting findings in stakeholder meetings and facilitating discussions to drive consensus on operational improvements
Conduct regular system audits to monitor data integrity, system health, and key performance metrics (e.g., approval cycle times, contract turnaround)
Track key dates and milestones; proactively identify and escalate potential risks, such as approaching deadlines, renewal windows, or expiring terms requiring action
Compliance & Process Improvement Participate in assessing, refining, and executing on future business requirements for the CLM system; contribute to template and playbook updates based on recurring issues and counterparty redline patterns
Support compliance with life sciences regulatory requirements (FDA, GxP where applicable) by ensuring contract workflows and documentation meet audit and traceability standards
Identify and recommend process improvements to enhance efficiency, compliance, and user adoption across the contracting process