The software vendor added Cyril Paciullo last week as one of its MVPs for Windows Live.
The MVP programme identifies developers who provide technical expertise for communities supporting Microsoft products and technologies. The title has been awarded to about 2,600 developers worldwide.
Paciullo's ties to the malware scene had angered at least one fellow Microsoft MVP.
"Microsoft is rewarding someone who has an active involvement with one of the most maligned names in PC hijacking. If that isn't booberific, I don't know what is," said Christopher Boyd, a Microsoft security MVP and director of malware research at Facetime Security Labs.
Paciullo operates in the grey area between legitimate software and illegal adware; the Messenger Plus application discloses that it comes bundled with a "sponsor programme".
The pop-up ads fail to identify their source to the end user, and the application installs deceptive icons on the user's desktop claiming to offer an online security scan.
Microsoft said that it was not aware of the spyware ties in the Messenger Plus application and pulled Paciullo's status once it was notified.
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