Microsoft 365 Setup Guide

A comprehensive, step-by-step guide for deploying and configuring Microsoft 365 for your organization. This guide covers all critical areas from initial tenant setup to advanced security policies.

What’s in this guide?

This guide is organized into four main areas. Follow them in order for a complete deployment.

1. Tenant Configuration

Set up your foundational Microsoft 365 tenant settings:

  • Custom domain (vanity domain) association
  • Organization and password policy settings
  • Emergency Access accounts
  • EOP & ATP baseline security
  • Alert policies

2. Azure AD Configuration

Secure your identity and access management:

  • Combined MFA + SSPR registration
  • Self-service password reset
  • User and guest settings
  • Admin consent controls
  • Conditional Access baseline policies

3. Microsoft Endpoint Manager

Manage and protect devices across your organization:

  • Device enrollment (Autopilot, MDM)
  • Compliance policies
  • App Protection (MAM) for mobile
  • Windows 10 Azure AD Join / Hybrid Join

4. Collaboration Governance

Control how users collaborate and protect sensitive data:

  • Data Loss Prevention (DLP)
  • Retention policies
  • Sensitivity labels
  • SharePoint & OneDrive sharing settings
  • Teams & Groups governance

Admin Monthly Report

Automated HTML report generated by PowerShell covering all key health metrics:

  • License usage, MFA coverage, inactive users, guest users
  • Conditional Access status, mailbox usage, admin roles, sign-in failures

Downloads — PowerShell Scripts

59 ready-to-use automation scripts covering all areas of this guide:

  • Setup Intune, Azure AD Conditional Access, Compliance, Exchange Online
  • Windows 10 security profiles, and Incident Response tools

Prerequisites

Before you begin, ensure you have:

  • A Microsoft 365 Business Premium or Enterprise license
  • Global Administrator access to your tenant
  • Your custom domain(s) ready for verification
  • Access to your DNS registrar

This guide was prepared based on Microsoft 365 best practices. Settings should be reviewed and adapted to your organization’s specific risk tolerance and compliance requirements.