In 2012, Bears general manager Jerry Angelo was fired. During the team's search, Emery was one of the four candidates, and was one of the two finalists for the job, along with Arizona Cardinals director of pro personnel Jason Licht. After being hired, Bears chairman George McCaskey told Emery that though head coach Lovie Smith's contract ran through 2013, and that Smith would be head coach in 2012, Emery would have the ability to make a change at the position after the end of the 2012 season. Smith was eventually fired on December 31, 2012 after the Bears missed the playoffs, despite having led the team to a 10–6 record. In Emery's first draft, he selected Shea McClellin, Alshon Jeffery, Brandon Hardin, Evan Rodriguez, Isaiah Frey, and Greg McCoy. Overall, critics had mixed reviews on Emery's debut draft, with the Chicago Sun-Times experts giving the draft an average "C" grade. On December 31, the Bears front office released long-time head coach Lovie Smith, and Emery began searching for a new head coach.
2013
On January 16, the Bears announced the hiring of Montreal Alouettes head coach Marc Trestman as head coach. Trestman was widely regarded as Emery's pick due to his cerebral approach to the game and ability to improve the performance of the quarterbacks he has worked with. In Emery's second draft, he selected G Kyle Long in the first round, LB Jon Bostic, LB Khaseem Greene, OL Jordan Mills, DE Cornelius Washington, and WR Marquess Wilson. Reaction was mixed with ESPN's Mel Kiper Jr. giving the whole of the Bears draft a C+ overall grade, stating the late round picks lacked value. However Jason Chilton rated the individual picks more highly in the later rounds. The Bears ended the season with an 8–8 record and failed to make the playoffs.
2014
In Emery's third draft he selected CB Kyle Fuller in the first round, DT Ego Ferguson, DT Will Sutton, RB Ka'deem Carey, S Brock Vereen, QB David Fales, P Pat O'Donnell, and OT Charles Leno, Jr.. The Bears traded with the Denver Broncos, swapping the Bears fifth round picks in 2014 and 2015 for the Broncos 4th and 7th picks in 2014. This ended up giving the Bears no fifth round pick, but two additional picks in both the fourth and sixth rounds. Emery also brought in undrafted free agentsJordan Lynch and James Dunbar. Bucky Brooks of NFL.com gave the Bears draft a B, and called the 4th round pick of Carey the draft's biggest steal. Additionally, Elliot Harrison of NFL.com ranked the Bears offseason moves as the second best in the league based on a strong draft and the additions of free agents DE's Jared Allen, Willie Young, Lamarr Houston, Israel Idonije, and QB Jimmy Clausen. On December 29, 2014, Emery was fired from the Bears after the team merited a 5–11 record, their worst since their debut year with Lovie Smith, and, once again, missed the playoffs. A significant, contributing factor to Emery's demise was his directive to extend quarterback Jay Cutler's contract in January 2014 to a lucrative seven-year deal with $126.7 million, of which $54 million was guaranteed. This negotiation has been deemed to be the worst contract in the NFL. The Bears hired Ryan Pace on January 8, 2015 to replace Emery as the GM.