Microsoft 365 Admin Alert: Critical September 30 Deadlines and Upcoming Changes You Can’t Ignore
Microsoft 365 administrators have a busy roadmap ahead, and September 30 is shaping up to be one of the most important dates of the year. Alongside two critical deadlines, Microsoft is rolling out several significant changes that will impact identity management, authentication, storage, and the overall user experience.
Organizations that fail to prepare could face synchronization issues, authentication challenges, and unexpected support requests from end users.
Let’s break down what requires attention and what actions your team should take now.
1. Entra Connect Sync Support Deadline
One of the most urgent items involves Microsoft Entra Connect Sync.
Any server running a version earlier than 2.5.79.0 will stop synchronizing identities after September 30. If your environment still relies on an older release, user and group changes in Active Directory may no longer synchronize with Microsoft 365.
Recommended Actions
- Verify the version of Entra Connect Sync currently deployed.
- Schedule upgrades immediately if running a version earlier than 2.5.79.0.
- Test synchronization after the upgrade to confirm successful operation.
Priority: 🔴 High
2. Conditional Access Custom Controls Changes
Microsoft is also introducing restrictions for Conditional Access custom controls.
Starting September 30, administrators will no longer be able to create or modify custom controls. While existing controls will continue functioning, Microsoft recommends beginning the transition toward External MFA solutions.
Custom controls are scheduled to reach end of life in May 2027, making early planning essential.
Recommended Actions
- Inventory existing Conditional Access policies.
- Identify policies that rely on custom controls.
- Develop a migration strategy toward External MFA integrations.
Priority: 🔴 High
3. Passkeys Become the Default Authentication Method
Microsoft continues its push toward passwordless authentication.
Beginning September 1, passkeys become the default authentication method in Microsoft Entra. Users who currently rely on SMS or voice authentication may be automatically enabled for passkey-related experiences.
Additionally, Microsoft plans to retire Microsoft-provided SMS and voice authentication on February 1, 2027.
Why It Matters
Passkeys offer:
- Stronger phishing resistance
- Improved user experience
- Enhanced security posture
- Reduced dependence on traditional MFA methods
Recommended Actions
- Review your organization’s MFA roadmap.
- Educate users on passkey adoption.
- Begin reducing dependency on SMS and voice authentication.
Priority: 🟠 Medium to High
4. New SharePoint and OneDrive Hero Link Experience
Microsoft is rolling out an updated Hero Link experience for SharePoint and OneDrive users.
The rollout is expected to occur between mid-September and late October.
What to Expect
- Updated visual layout and user experience.
- Changes that may generate support tickets from end users.
- Potential communication requirements for adoption and awareness.
Recommended Actions
- Review Microsoft’s preview documentation.
- Notify help desk and support teams.
- Update internal user guides if applicable.
Priority: 🟡 Medium
5. Auto-Expanding Archive Capacity Doubles
Organizations using Exchange Online archiving will welcome this enhancement.
Microsoft is increasing the maximum archive size from 1.5 TB to 3 TB, with rollout beginning in October.
Benefits
- Increased long-term storage capacity.
- Reduced concerns about archive limits.
- Better support for retention and compliance requirements.
Recommended Actions
- Review archive growth trends.
- Update storage planning documentation.
- Communicate benefits to compliance and records teams.
Priority: 🟡 Medium
6. SharePoint Pay-As-You-Go Storage
Microsoft is preparing to roll out SharePoint Pay-As-You-Go Storage beginning in November.
This new model provides organizations with additional flexibility for handling growing storage requirements beyond allocated quotas.
Recommended Actions
- Review current SharePoint storage utilization.
- Forecast future storage growth.
- Evaluate potential budget impacts.
Priority: 🟡 Medium
Immediate Administrator Checklist
Before September 30, Microsoft 365 administrators should:
✅ Verify Entra Connect Sync version compliance
✅ Identify Conditional Access custom controls in use
✅ Review and modernize MFA strategies
✅ Begin planning for passkey adoption
✅ Prepare support teams for upcoming SharePoint and OneDrive changes
✅ Assess future storage requirements for SharePoint and Exchange Online
Final Thoughts
September 30 is more than just another date on the Microsoft 365 roadmap. While the Entra Connect Sync and Conditional Access custom control deadlines require immediate action, the broader shift toward passwordless authentication, expanded archive storage, and evolving SharePoint capabilities signals a larger transformation across the Microsoft ecosystem.
Organizations that take a proactive approach now will avoid last-minute disruptions and position themselves for a smoother transition into Microsoft’s next generation of identity and collaboration services.
The deadline is approaching quickly. Make sure your environment is ready before September 30 arrives.