Senior Engineer, AI and Automation

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 the 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.

Senior Engineer, AI & Automation Cambridge, MA (Hybrid)

Position Summary: 

Flagship Pioneering is building the infrastructure and engineering foundation to make AI a force multiplier across the company. This role sits within IT's Digital Platforms team and operates at the intersection of AI infrastructure, automation engineering, and enterprise use case delivery. You'll work directly with the Enterprise AI team and Digital Platforms to productionize AI capabilities at scale, including MCP (Model Context Protocol) builds and integrations, agentic tooling, and cross-functional automation pipelines.

This is a high-ownership, hands-on engineering role. You will own the build and deployment of AI-powered workflows and systems across business functions, from intake through production. You'll also help establish the platform and tooling foundations that enable the broader organization to operate AI responsibly and at speed.

What You'll Do

• Design, build, and deploy AI use cases across Flagship business functions, including finance, legal, HR, research, and operations
• Maintain AI infrastructure and automation platforms: MCP server builds and integrations, agentic frameworks, LLM (Large Language Model) orchestration, and low-code/no-code tooling (e.g., Zapier, Workato)
• Partner with the Enterprise AI Lead to scope and accelerate the AI use case portfolio, moving requests from triage to production
• Build and maintain integrations between AI tools and enterprise systems (Coupa, NetSuite, Slack, M365, and others)
• Establish MLOps platform to establish deployment, observability and feedback loops for deployed AI workflows: usage monitoring, output quality tracking, and prompt iteration cycles
• Support evaluation and implementation of AI-enabled SaaS tools, including proof-of-concept builds and vendor assessments
• Contribute to AI governance infrastructure: usage monitoring, ZDR (Zero Data Retention) compliance checks, sandbox governance, and documentation
• Collaborate with Information Security on AI security posture, including data exposure risk, agentic workflow guardrails, and shadow AI detection

What We're Looking For

• At least 5 years of technical delivery experience
• At least 4 years of software (python preferred) and automation engineering experience, with experience building and shipping LLM-based systems to production
• At least 2 years' experience with cloud first architectures (AWS preferred)
• At least 2 years' experience building and launching applications and solutions using standard DevOps and MLOps tools.
• Hands-on development experience with LLM APIs (Anthropic, OpenAI, or similar) including prompt engineering, tool use, and multi-step agentic workflows
• Building experience with MCP and other agentic tool frameworks
• Familiarity with maintaining RAG (Retrieval Augmented Generation) architectures, vector databases, and document ingestion pipelines
• Working knowledge of enterprise systems including ERP (Enterprise Resource Planning), HRIS (Human Resource Information Systems), and experience with enterprise automation platforms (Zapier, Workato, Make, or equivalent)
• Ability to build integrations across SaaS systems using APIs, webhooks, and event-driven architecture
• Strong judgment about when to build vs. buy, and how to scope an MVP vs. a production system
• Able to identify high-leverage automation opportunities independently and push back on low-impact requests with clear reasoning
• Clear communicator w