He received the O'Riordan-Mundy Distinguished Legal Service Award in 1999 and remained on the City Council until he was appointed Suffolk County's 14th district attorney by Acting Governor Jane Swift on February 19, 2002.

In an effort to ensure that the historical wrongful convictions that came to light under his leadership never reoccurred, Conley assigned his top courtroom prosecutor to join with ranking police officials, prominent defense attorneys, and the nation's leading academic expert on eyewitness identification to review the investigative processes by which eyewitness evidence was gathered and recommend changes that would minimize the likelihood of faulty identifications.

The reforms prompted defense attorney Barry Scheck of the Innocence Project[9] to cite Boston and Suffolk County as being "at the forefront of the country" [10] in averting wrongful convictions, and eyewitness evidence expert Gary Wells to call them the "Gold Standard.

"[11] "The policies he implemented [...] went beyond what even what the US Department of Justice had been recommending and provided a model not only for law enforcement but for the Supreme Judicial Court as well," the Boston Bar Association wrote.

[12] Shortly after taking office, Conley implemented a policy of assenting to any reasonable request for post-conviction testing of DNA evidence that was unavailable at the time of a defendant's trial.

[15] Under Conley's stewardship, the Suffolk District Attorney's Office partnered with numerous service providers, government agencies, and victim advocacy groups to build the Family Justice Center of Boston.

[16] The FJCB streamlines services for victims of child abuse, intimate partner violence, and sexual crimes by coordinating the responses of numerous agencies and providers – including police, prosecutors, social workers, and others – under one roof.

[21] Yet with his departure occurring as lawmakers were considering an overhaul to the criminal justice system that would reduce the number of people incarcerated,[21] Conley surprised political observers on September 12, when he announced that he would be resigning, with three months left of his term, to take a job at Mintz Levin, a leading law firm in Boston, and at its lobbying subsidiary, ML Strategies.

[22] This decision arrived shortly after Greg Henning, who Conley had endorsed as the Democratic candidate for District Attorney, lost the election to Rachael Rollins.