The future of general manager Alex Anthopoulos has been the subject of much speculation in recent weeks. He overhauled the roster two years ago but the Blue Jays have gone 157-167 since and extended their playoff drought to 21 years with an 83-79 finish this past season.
"Alex I can say for a fact is back," Beeston said Friday in an interview on Sportsnet 590 The Fan.
Anthopoulos has been with the franchise for over a decade and has served as GM for the last five years.
"He hasn't finished what he started out to do," Beeston said. "I'm 100 per cent supportive of him. I think that he has done a very good job. I think we are now seeing the benefits of what happened with his development (and) his investment in the farm system.
"I think that's only going to be better for the future."
Beeston also said he expected manager John Gibbons to return next year. Anthopoulos has also voiced his confidence in the Blue Jays skipper, who has a rolling contract that kicks in every Jan. 1.
The Blue Jays had a strong first half in 2014 but struggled after the all-star break and fell out of the playoff picture last month.
Beeston said the team's payroll of about US$135-137 million will rise in 2015. The 69-year-old native of Welland, Ont., also confirmed that he's in the last year of his contract but said he has no plans to leave the organization.
"I'm here as long as Rogers wants me here," he said. "I enjoy what I'm doing."
Also Friday, the Blue Jays announced they have outrighted infielder Munenori Kawasaki, first baseman Dan Johnson and catcher George Kottaras to triple-A Buffalo. Johnson and Kottaras, a Toronto native, have both elected free agency.