Why Many IT Teams Still Run Both Intune And Configuration Manager

A new report suggests IT teams run both concurrently as they strive to alleviate modern endpoint management complexities.

Microsoft has spent about a decade positioning Intune—its cloud-based endpoint management platform—as the future of endpoint management. While Intune is widely adopted in Microsoft environments, a new report suggests IT teams aren’t quite ready to give up Configuration Manager (ConfigMgr) just yet.

According to Recast Software’s 2026 State of Intune report, 62 percent of organizations manage endpoints using both Intune and ConfigMgr, while more than half of organizations still using ConfigMgr have no plans to retire the tool.

The findings suggest that despite Microsoft’s cloud-first management push, many IT teams view hybrid endpoint management as an operational necessity rather than a transition state.

For Many IT Teams, Co-Management Has Become The End State

“Hybrid stopped being a transition state and became the destination,” Jake Mosey, chief product officer at Recast Software, told MES Computing. “The market has spent a decade treating co-management as a finite period of time. The question isn’t how do we get everyone to the other side, it’s what an operational layer looks like when it has to work consistently across both, for years, with limited resources.”

The survey found strong overall sentiment toward Intune, with 81 percent of respondents reporting a positive view of the platform. Yet organizations continue to devote substantial time to manual management tasks. Recast Software found that roughly two-thirds of respondents spend between six and 15 hours each week on packaging, patching, troubleshooting and reporting activities.

Application packaging and deployment were cited as the biggest challenges by 37 percent of respondents, followed by third-party patching at 33 percent.

For many midsize organizations, those challenges help explain why Configuration Manager remains part of the endpoint management toolkit.

One midmarket IT leader, who asked not to be named, recently completed a migration from a hybrid environment to full Intune-based management said Configuration Manager continued to provide benefits in tasks such as server management, Active Directory administration and software deployment.

“What stopped us in the past was with ConfigMgr we were able to manage both servers and workstations all in one place,” the IT leader said. “Certain policy configurations could be pushed more easily with ConfigMgr if you are still relying on Active Directory, and patch and application deployments were more reliable via ConfigMgr.”

The organization ultimately migrated because it wanted to reduce dependence on on-premises infrastructure and take advantage of cloud-native capabilities, including Autopilot device provisioning, mobile device management and broader support for hybrid work.

The move did not eliminate complexity, though.

The IT leader said the organization ultimately acquired another endpoint management platform to handle patching across servers, workstations, Linux systems and third-party applications, while also replacing some remote support capabilities.

“In the end, we are only using Intune for asset management, certain security policy management, Defender configuration and BitLocker key management and another solution for everything else,” the IT leader said. “It’s not necessarily cheaper, but it allows us to ensure systems are configured properly anywhere as we still are in a hybrid work environment.”

Mosey said many organizations continue operating both management platforms because each offers strengths that remain difficult to replace.

“CM [Configuration Manager] still does a lot of things very well, as does Intune,” he said. “IT teams are resource-constrained and aren’t going to fix something that isn’t broken, especially if they are constantly being reactive."

The survey found that nearly four out of five respondents described their work as mostly reactive, while roughly half said only two or three people manage their Intune environments.

Those staffing realities may be particularly relevant for midsize organizations.

Endpoint Management Lesson For The Midmarket

“It is more common for smaller or midsize organizations to commit to the more modern management solutions with Intune,” Mosey said. “Larger organizations can handle more complexity, and choosing the right tool to solve the problem sometimes means multiple solutions.”

Still, the survey suggests that cloud-native endpoint management adoption may be progressing more slowly than many industry observers expected. According to Recast Software, only 10 percent of respondents reported that more than 76 percent of endpoints are fully managed by Intune.

To be clear, Microsoft addresses co-managing Windows devices with both Intune and Configuration Manager. Windows system admins can select which group of devices are managed by either, according to documentation on Microsoft Learn. This gives organizations some flexibility in endpoint management.

However, for midsize IT leaders, the findings reinforce a practical lesson: Endpoint management isn’t simply a choice between cloud and on-premises tools. Instead, many organizations employ a mix of platforms to balance modernization goals, support hybrid workforces, and stretch limited IT resources. Intune may be a rising star, but Configuration Manager is still doing a lot of heavy lifting.