A Safehouse is a location in Alpha Protocol in which Michael Thorton can use the computer to check e-mails and access The Clearinghouse to purchase weapons. A television is used to watch the news. Thorton can also check missions and change his wardrobe without hostiles nearby. As you progress through the game, safehouse trophies will be available and found throughout each safehouse.
- Madison Saint James is the only person the player ever sees or speaks to inside a safehouse outside of a cutscene.
- Mina claims that although Alpha Protocol owns each safehouse, they have so many resources that they don't actually know about each individual safehouse. This means that every safehouse of the agency is hidden until searched for whenever needed.