Lead Engineer, Microsoft 365 and Identity Automation

Flagship Pioneering•Cambridge, MA

About The Position

Flagship Pioneering is seeking a hands-on Lead Engineer to own the code and automation supporting its shared Microsoft 365 and Entra ID environment, which serves dozens of portfolio companies with distinct identity, domain, and lifecycle needs. This is an individual contributor engineering role focused on maintaining and extending existing codebases and integrations, ensuring identity lifecycle management continues to work as business requirements change, and serving as a senior escalation point when automation or tenant behavior breaks. The role is not focused on architecture or people management. The engineer will build and maintain production automation using Microsoft Graph, PowerShell, supported APIs, Python tooling, and integration platform workflows. The work includes identity lifecycle processes; Exchange Online and SharePoint Online administration; Entra identity governance and access capabilities; and integrations among HR, ITSM, identity, and collaboration systems. Engineering practices include source control, peer review, testing, change control, monitoring, CI/CD, runbooks, support documentation, and secure least-privilege authentication. The salary range is $128,000–$176,000. Compensation depends on factors including qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, an annual incentive program, retirement benefits, and a broad range of other benefits. The company states its commitment to equal employment opportunity and building diverse and inclusive teams.

Requirements

At least 6 years of experience engineering and supporting Microsoft 365 and Entra ID environments, including at least 3 years developing and maintaining production automation using Microsoft Graph.
Advanced PowerShell experience, including the Microsoft Graph PowerShell SDK and Exchange Online PowerShell, and working proficiency in another scripting or programming language.
Demonstrated experience inheriting, troubleshooting, refactoring, and supporting existing production codebases.
Hands-on experience with Entra identity lifecycle management, groups and licensing, app registrations, service principals, Conditional Access, PIM, B2B identity, SSO, and SCIM provisioning.
Experience automating Exchange Online administration and working with SharePoint Online administration or automation.
Working knowledge of REST APIs, OAuth 2.0, JSON, Git-based workflows, code review, testing, monitoring, and unattended authentication.
Broad Microsoft 365 operational knowledge, including troubleshooting complex issues across Entra ID, Exchange Online, Intune, SharePoint, and Teams.
Strong problem-solving, documentation, and communication skills, including the ability to lead technical work and explain tradeoffs to technical and nontechnical stakeholders.

Nice To Haves

Experience with Workato or a comparable integration platform such as Power Automate, Azure Logic Apps, MuleSoft, or Boomi, or demonstrated ability to work effectively with integration and low-code automation platforms.
Experience with Entra ID Governance, HR-driven identity integration, or multi-company and multi-domain Microsoft 365 environments.
Experience supporting company launches, mergers, divestitures, tenant transitions, or other complex organizational lifecycle events.
Experience with Azure Automation, Azure Functions, Key Vault, CI/CD pipelines, infrastructure as code, or configuration as code.
Experience with CoreView, ShareGate, or comparable Microsoft 365 administration, migration, and governance tools.
Experience in regulated environments such as life sciences, GxP, or HIPAA.
Relevant certifications such as SC-300, MS-102, AZ-104, or AZ-500.

Responsibilities

Build, maintain, and extend production automation using Microsoft Graph, PowerShell, and supported APIs.
Own existing scripts, integrations, and services by resolving defects, reducing technical debt, documenting solutions, and updating code as identity sources, attributes, domains, and organizational requirements change.
Engineer secure and reliable automation using appropriate API patterns, monitoring, logging, error handling, and least-privilege authentication, including app registrations, service principals, managed identities, certificates, and properly scoped permissions.
Maintain and improve Exchange Online and SharePoint Online automation for mailboxes, groups, permissions, domains, mail flow, site provisioning, sharing, and lifecycle management, including changes related to portfolio company launches, mergers, renames, and other lifecycle events.
Maintain accurate joiner, mover, and leaver processes for employees and contractors across Flagship and its portfolio companies, including provisioning, groups, licensing, access changes, and deprovisioning.
Engineer and support Entra capabilities including Lifecycle Workflows, identity governance, dynamic groups, Privileged Identity Management, Conditional Access, B2B identity, single sign-on, and SCIM provisioning.
Build and maintain integrations among HR, ITSM, identity, and collaboration systems using Microsoft Graph, native Microsoft capabilities, custom code, or integration platforms such as Workato when appropriate.
Apply engineering practices including Git-based source control, peer review, testing, change control, monitoring, CI/CD, runbooks, and clear support documentation.
Mentor peers and serve as a senior escalation point for complex Microsoft 365 and identity issues, resolving root causes through code, configuration, or native platform capabilities.