The Korean company has agreed to pay the computing giant royalties for the technology used in its Android devices, and will in turn help to develop and market Windows Phone handsets, CNET reports.
Microsoft and Samsung are thought to have signed the agreement to avoid the potential litigation that other technology firms have encountered. Microsoft previously signed a similar deal with phone manufacturer HTC.
Samsung has invested heavily in the Windows Phone line in the past, but has since pledged much of its resources to Google's Android software, which powers its flagship Galaxy SII smartphone.
"Microsoft and Samsung see the opportunity for dramatic growth in Windows Phone, and we're investing to make that a reality," said Andy Lees, president of the Windows Phone division.
Samsung's recently released Omnia W Windows Phone is the first of the manufacturer's handsets to run the new Mango edition of the operating system.
Elsewhere, the company is locked in an ongoing legal battle with Apple in territories across the globe.