The major difference between the two is the type of desktop. XenApp delivers a one-to-many Windows Server (e.g. Windows Server 2008 or 2012) machine that is shared by many users. XenDesktop delivers a one-to-one Windows desktop machine (e.g. Windows 7 or 10) that is used by a single user.

At a high level, this fundamental difference has meant:

1. XenApp users share the CPU, GPU, memory, and disk resources with all of the other users on the same server. XenDesktop users get their own private CPU, GPU, memory, and disk, leveraging the hypervisor’s ability to allocate, isolate, and protect these resources on a per VM basis.
2. XenApp users get a Windows Server look and feel (unless the Windows Desktop Experience feature is used). XenDesktop users get a Windows desktop look and feel.
3. XenApp users share access to all of the applications installed by IT on the XenApp server they are logging into (i.e. if 200 users logon to the same XenApp server, all 200 users get the same apps). XenDesktop users get access only to the apps installed on their individual desktops (i.e. each user can have their own unique apps).
4. XenApp users can be given a minimal amount of personalization if IT uses a profile management tool to restore their settings each time they logon. XenDesktop users can be given full personalization, including one-off apps and plug-ins if IT assigns a persistent virtual desktop to each user.
5. XenDesktop supports server based OS and desktop based OS whereas XenApp only supports server based OS.