The new guidelines cover everything from police recruitment practices to policies on use of force. The department was harshly criticized by Obama's Justice Department for civil rights violations.
A day after three officers were acquitted of trying to cover up the killing, Jason Van Dyke was sent to prison for shooting the black teen 16 times. McDonald's family argues the punishment is light.
Final arguments were given on Thursday in the murder trial of a Chicago police officer who shot a 17-year-old youth in 2014. The shooting sparked weeks of unrest and resulted in political fallout.
The Cook County grand jury indictment alleges that the three police officers were at the scene of the killing and worked together to conceal crucial facts in order to protect a fellow officer.
The investigation found widespread evidence of unconstitutional use of force. It was launched more than a year ago after a black teenager was shot and killed by a white Chicago police officer.
Chicago Mayor Rahm Emanuel says the new Civilian Office on Police Accountability will be independent, but critics say it will still answer to city hall.
The city's inspector general recommended that 10 officers be fired in connection with the 2014 killing of 17-year-old McDonald. Several of those officers have since retired or resigned.
Chicago's head of police announced his recommendation to dismiss the officers Thursday. Superintendent Eddie Johnson cited allegations that they gave false reports on the 17-year-old's shooting death.
The Independent Police Review Authority is charged with investigating police shootings and misconduct in the city — but has been criticized for acting slowly and rarely doling out disciplinary action.
A report commissioned by Mayor Rahm Emanuel blames racial bias and a "code of silence" for the city's "broken" police system.