In the editorial, titled "At Home with Jennifer Aniston," the former Friends star appears in all photos solo, while Theroux is also pictured on his own, walking away from the house.
There are few signs of Theroux’s presence inside the $21 million mansion in the photos published by the magazine.
“There was barely anything showing that Justin resided there,” a source told The Daily Mail. “It soon become clear that it was entirely her place and not his.”
In the bedroom, four photos of the couple can be seen, and two are older, taken in 2011 -- four years prior to their wedding.
Aniston admitted to Architectural Digest that she struggled to involve Theroux in remodeling her home.
“Justin definitely wanted to be involved, so there was a bit of a learning curve for me on how to include another voice in the design process,” Aniston said. “For instance, I figured out that immediately saying ‘No!’ to any suggestion is not the most collaborative move."