Enterprise Applications Business Analyst

Flagship Pioneering is a life sciences innovation enterprise that creates and funds breakthrough companies developing pioneering biotechnologies. Our ecosystem thrives on innovation, and our security strategy is fundamental to protecting our intellectual property and enabling cutting-edge scientific discovery.

Overview

We are seeking a detail-oriented and analytical Enterprise Applications Business Analyst to join our growing Enterprise Applications team at Flagship Pioneering. This role will provide critical support across core business systems—including UKG, Netsuite, Greenhouse, Cobblestone, Coupa, Notion, and ADP—helping ensure they run smoothly and continue to evolve with the needs of our business. The ideal candidate will act as a bridge between business stakeholders and technical teams, supporting operations, gathering requirements, analyzing data, and driving process improvements through actionable insights.

Responsibilities

• Support the Business Relations Manager in engaging with business stakeholders (HR, Finance, Procurement, IT), ensuring alignment between stakeholders and technical teams on enterprise application initiatives. 
• Gather, document, and validate business requirements for system enhancements, integrations, and new capabilities.
• Provide day-to-day application support and troubleshooting across HCM, ERP, ATS, CLM, Procurement, and Payroll systems.
• Collaborate with vendors and internal IT teams to resolve issues, implement fixes, and manage upgrades/releases.
• Analyze system usage, business processes, and workflows to identify areas for optimization and automation.
• Develop and maintain dashboards and reports using Power BI to deliver actionable insights for HR, Finance, and business leaders.
• Partner with business units to design and test system configurations, ensuring accuracy and alignment with business processes.
• Support system data governance, ensuring data accuracy, compliance, and reporting consistency.
• Assist with project management activities, including requirements documentation, test planning, and user acceptance testing.
• Provide end-user training, documentation, and support for new processes and system enhancements.

Qualifications

• Bachelor’s degree in Information Systems, Business, or a related field (or equivalent work experience).
• 3+ years of experience as a Business Analyst or in a similar role supporting enterprise applications.
• Hands-on experience with one or more enterprise systems (HCM, ERP, ATS, CLM, Procurement, Payroll).
• Strong proficiency with Power BI (or similar BI/reporting tools) for building dashboards and visualizations.
• Solid understanding of business processes in HR, Finance, and Procurement functions.
• Experience working with integrations across multiple enterprise applications (Workato or similar a plus).
• Familiarity with SDLC and Agile project methodologies.
• Strong analytical skills with attention to detail and problem-solving mindset.
• Excellent communication skills with the ability to translate business needs into technical requirements.
• Ability to work collaboratively in a fast-paced, cross-functional environment.

Preferred Skills

• SQL experience for querying and validating data.
• Exposure to data governance practices and compliance frameworks.
• Experience with vendor management and SaaS solution support.
• Knowledge of reporting for compliance, audit, and financial operations.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

Recruitment & Staffing Agencies:  Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates.  The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team.   Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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