Microsoft Configuration Manager and Intune are two solutions that cater to different application packaging and deployment requirements. This article will compare the effectiveness of Configuration Manager and Intune for application packaging and deployment with a brief overview of their functionalities.

Configuration Manager

Configuration Manager, previously known as SMS, SCCM, and Endpoint Configuration Manager, is a Windows device management solution that provides granular control over application deployment. It can manage domain-joined on-premises Windows devices and can be extended to cloud-joined devices via Co-Management and a Cloud Management Gateway (CMG).

Supported Application Types: Configuration Manager natively supports MSI, MSIX, AppX, executable installers, Edge for Business, M365 app suite, and App-V packages.

Application Installs, Updates, and Deployment: Configuration Manager allows for deployment during imaging, forced installation, or self-service through Software Centre. Applications can be targeted based on Collections, offering granular control over application distribution. Configuration Manager’s reporting functionality is comprehensive, enabling detailed insights through SQL-based query tools.

Important Considerations: Configuration Manager does not support Microsoft Store apps natively and requires co-management with Intune. Additionally, it has fewer features compared to Intune, with its development focusing primarily on bug fixes and minor improvements.


Microsoft Intune is a cloud-based Mobile Device Management platform that supports various devices, including Windows, Android, iOS, macOS, and Linux. It enables seamless device management without needing on-premises networks, making it ideal for organizations with remote workforces.

Supported Application Types: Intune supports MSI Line-of-Business, MSIX, AppX, Store for Business, and Win32 executable apps. However, it does not support App-V packages.

Application Installs, Updates, and Deployment: Intune enables application installation in the System or User context and supports application supersedence for Win32 applications. Applications can be targeted based on Azure AD groups, which can be static or dynamic. Intune also supports filters for more refined targeting. Applications can be installed during “imaging,” forced, or made available via the Company Portal application.

Important Considerations: Intune’s reporting functionality is less granular than Configuration Manager, requiring more navigation through the portal or use of Graph API. However, Intune is fully supported for Virtual Desktop Infrastructure (VDI) management in Azure Virtual Desktop (AVD) and Windows 365.


The choice between Configuration Manager and Intune depends on an organization’s specific needs and infrastructure. Configuration Manager is better suited for organizations with extensive on-premises infrastructure, while Intune is ideal for those seeking a cloud-based management solution. Evaluating supported application types, deployment flexibility, control granularity, and future development will guide organizations in choosing the best solution. Co-management may offer the optimal balance, leveraging the strengths of both Configuration Manager and Intune.