Terms were not announced.
Bills GM Brandon Beane said this is a "reset" for Trubisky and that he doesn't expect the No. 2 pick in 2017 to be a long-term option behind Allen.
"I don't know what went on in Chicago, but he started 50 games," Beane said of Trubisky. "... I think the label has been put on Mitchell from afar that maybe he doesn't deserve it. This is a reset for him. We don't expect him to be here long term."
Trubisky, 26, began the 2020 season as the Bears' starting quarterback before losing the job to Nick Foles in Week 3, only to finish out the season as the starter, reclaiming the job in Week 12. He finished the season with 2,055 yards, 16 touchdowns and 8 interceptions, while completing 67% of his passes.
Beane said the Bills will approach Allen sometime after the NFL draft -- in May or possibly in the summer -- about an extension, confirming the team's interest in getting a deal done this offseason.
Trubisky's future in Chicago had been tenuous since the Bears traded for Foles last April and declined Trubisky's fifth-year option a little more than a month later.
Still, Trubisky expressed a willingness to return to Chicago for the 2021 season, telling reporters in the aftermath of the season-ending playoff loss to the New Orleans Saints that he had "unfinished business" with the team.
He had been under the microscope in Chicago since the Bears traded up to select him. While Trubisky has had an up-and-down four NFL seasons, quarterbacks Patrick Mahomes (drafted 10th overall in 2017) and Deshaun Watson (12th overall) have developed into franchise quarterbacks.
Trubisky went 29-21 as a starter in Chicago, throwing for 10,609 yards with 64 touchdowns and 37 interceptions while completing 64% of his passes. He also rushed for 1,057 yards and eight touchdowns. He was a Pro Bowl selection in 2018 when he set career highs in passing yards (3,223) and touchdown passes (24).
ESPN's Marcel Louis-Jacques and Jeff Dickerson contributed to this report.