Reports last week indicated that Beeston was on his way out of the Blue Jays' front office, with Baltimore Orioles executive vice president Dan Duquette and Chicago White Sox executive vice president Ken Williams both linked to Toronto.
At this week's winter meetings in San Diego, Duquette said he was focused on helping the Orioles rebuild.
The White Sox reportedly denied Williams permission to interview with the Blue Jays.
According to Buster Olney of ESPN, the Blue Jays' ownership "was not pleased" with some of Beeston's actions during the search for a replacement for MLB commissioner Bud Selig.
Beeston, 69, was the first employee hired by the Blue Jays in 1976 and has been the club's president and CEO since 1989. He moved to the commissioner’s office in 1997 and returned to the Jays in 2009.