Associate Controller Jobs in Franklin, MA (NOW HIRING)

Who We Are
Flagship Pioneering is a biotechnology company that invents and builds platform companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble capital to allow them to take courageous leaps. Those big leaps in human health and sustainability exponentially accelerate scientific progress in areas ranging from cancer detection and treatment to nature-positive agriculture.
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 scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform 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 twice named to Fast Company's annual list of the World's Most Innovative Companies.
Position Summary
The Associate Director, Finance, will be a key member of the Flagship Pioneering finance team, responsible for supporting financial planning, reporting, accounting, forecasting, and operational finance activities across primarily the Pioneering Medicine's (PM) portfolio of internal and partnered programs. This individual will partner closely with PM leadership, program teams, functional leaders, and cross-functional finance and accounting stakeholders to provide financial insight, strengthen budget discipline, and support timely, high-quality decision-making in a dynamic biotechnology environment.
The role will manage core finance activities across assigned PM entities and programs, including budget-to-actuals, cash flow monitoring, management reporting, forecasting, close support, collaboration partner reporting, and ad hoc analysis. The Associate Director will also help improve finance processes, reporting standards, systems, and controls.
While this role is primarily focused on the Pioneering Medicines business unit, the successful candidate should also bring strong accounting and controllership capabilities and be able to provide cross-functional support to Flagship Labs or related portfolio company finance teams as business needs require. This may include supporting close review, GAAP compliance, audit readiness, financial statement analysis, accounting operations, and process improvement initiatives in partnership with the broader finance organization.
Key Responsibilities

• Serve as a finance partner to Pioneering Medicines leadership, program teams, functional leaders, and cross-functional stakeholders, providing financial insights that support portfolio, program, and business decision-making.
• Manage financial planning, forecasting, reporting, and analysis for assigned PM entities, asset companies, internal programs, and partnered programs, including budget-to-actuals, variance analysis, cash flow monitoring, and management reporting.
• Lead or support monthly, quarterly, and annual close activities, including accruals, journal entry and reconciliation review, financial reporting, flux analysis, and coordination with accounting and finance operations teams to ensure timely and accurate results.
• Partner with Program Managers and functional leaders to develop and maintain program-level budgets, forecasts, operational plans, and financial models, including support for new asset proposals, ongoing program funding, and portfolio prioritization.
• Support financial management of research collaborations, partnered programs, and external pharma relationships, including collaboration budget tracking, reporting requirements, forecasting, joint finance meeting preparation, and review of relevant financial terms.
• Provide accounting and controllership support for PM, Flagship Labs, or related portfolio company needs as required, including GAAP compliance, audit support, financial statement review, close process support, ASC 842 lease accounting, capital project tracking, and accounting policy or process implementation.
• Coordinate with Finance Operations, Accounting, Tax, Legal, Business Development, and external consultants to support audits, tax compliance, statutory or fund reporting, K-1 reporting where applicable, collaboration agreements, financings, company transitions, and other complex or evolving business needs.
• Help develop, standardize, and improve finance reporting processes, close procedures, forecasting tools, systems, workflows, and internal controls to support scalability, accuracy, efficiency, and business visibility.
• Proactively identify financial, operational, reporting, or control-related risks and opportunities, and recommend practical solutions that balance business needs, finance requirements, and compliance expectations.
• Guide, mentor, and support junior finance or accounting team members, including providing review, coaching, and direction on financial analyses, close activities, reporting packages, process improvements, and project deliverables.

Minimum Qualifications

• BS/BA in accounting or finance; MBA is a plus. CPA Preferred.
• 10+ years of financial and accounting experience. Life sciences / biotechnology industry preferred.
• Strong understanding of US GAAP, financial reporting, accounting operations, month-end and quarter-end close processes, account reconciliations, accruals, and internal controls. IFRS experience is a plus.
• Experience with budgeting, forecasting, cash flow management, budget-to-actual analysis, variance analysis, and financial modeling across multiple entities, programs, or business units.
• Demonstrated ability to partner effectively with cross-functional teams, including R&D, program management, business development, legal, tax, accounting, finance operations, senior leadership, and external partners.
• Strong business acumen, with the ability to connect operational priorities, program strategy, contractual obligations, and financial outcomes.
• Ability to interpret complex financial information, identify key risks and drivers, and communicate insights clearly and decisively to both finance and non-finance stakeholders.
• Experience supporting research collaborations, partnered programs, portfolio companies, audits, tax compliance, statutory reporting, fund reporting, or external consultant coordination preferred.
• Working knowledge of financial systems and procurement tools; NetSuite and Coupa experience preferred.
• Flexible, collaborative, and solutions-oriented team player with strong project management skills, attention to detail, and the ability to manage multiple deliverables in a fast-paced, evolving environment.

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.
At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.
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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The salary range for this role is $148,000 - $203,500. 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.
Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.