If you connect your Microsoft account to Windows 10, it will automatically assume you want to enable every single app and feature that requires an account be connected. There are a whole host of things you cannot do unless you connect the account but it’s the features that self-activate that are the bigger problem. In Windows 10, like in Windows 8, there is an app called ‘Messaging’ which automatically signs in if you use your Microsoft account on the system. This app is practically barren with little to no settings and no way to turn it Off and yet, it populates with your Skype conversations. The lack of settings for the app include a ‘Sign Out’ option making it seem as though the only way to be rid of this app is to disconnect your Microsoft account from Windows 10 but fortunately, that isn’t the case. You can sign out of the Messaging app and here’s how.
The Messaging app populates with you Skype conversations and that should give a clue as to how you can sign out of it. Whenever you open the Messaging app, you will notice that a Skype Video window opens right away. Sometimes it will ask you to update information, and other times it will show you invitations to connect sent by other Skype users. We might impulsively dismiss this window if we aren’t looking to use Skype but this is how you sign yourself out of the Messaging app.
Instead of dismissing this window, look for the Settings option at the top left.
Sign out of the Skype video app by clicking the ‘Sign out’ option under the Account section and Messaging will be signed out as well.
There is unfortunately no way to opt out of using the Messaging app but still remain signed in on Skype. You can try and uninstall the Messaging app with a PowerShell command or use Skype’s desktop app.