Contracts Systems Manager

Flagship Pioneering is a scientific innovation engine that invents and builds 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 in human health, sustainability, and beyond. 

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 team of scientists, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and create breakthroughs 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 named four times to Fast Company’s annual list of the World’s Most Innovative Companies.

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. 

Key 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

Required Qualifications

• 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

Preferred Qualifications

• 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

Culture & Values (Flagship)

We seek individuals who reflect Flagship's culture of fearless exploration, entrepreneurial thinking, and collaborative impact. You thrive in environments that require creative problem solving, strong ownership, and alignment with mission-driven outcomes. 

Work Environment & Benefits

• Standard office environment in Cambridge with hybrid and remote flexibility options
• Collaborative, interdisciplinary teams engaged in high-impact innovation 
• Professional growth opportunities across Flagship Pioneering and its portfolio 
• Competitive compensation and benefits package

Equal Opportunity Employer

Flagship Pioneering is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, or protected veteran status. 

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The salary range for this role is $108,000 - $148,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Flagship Pioneering's good faith estimate as of the date of publication and may be modified in the future.