Keith Sandy and Dominique Perez were ordered to appear at a preliminary hearing, the date of which has not yet been set, said District Attorney Kari Brandenburg of New Mexico's Second Judicial Circuit.
Sandy and Perez are accused of killing James Boyd in March. The 38-year-old homeless man spent the night before his shooting in a shelter, but when the shelter closed for the winter, Boyd tried to camp in the hills above the city, officials said.
Overnight camping in the hills is illegal.
Helmet and body cameras worn by dozens of city police who converged on the campsite showed Boyd with two small camping knives in his hands.
Over several hours, Boyd talked with officers, at one point claiming to be "the Department of Defense."
The cameras captured officers converging on a small nest of rocks on the hillside. At one point, Boyd turned his back to the officers and they began firing.
Officers fired a shotgun and nonlethal beanbag pellets at Boyd, while other officers were caught on camera throwing flash-bang grenades. The video also shows one officer unleashing his K-9 German shepherd against Boyd.
The helmet cameras show Boyd wheezing for breath after the attack. He died later at a local hospital.
Sandy retired from the department in December of 2014, an Albuquerque police spokesman said. It's unclear if Perez is still on the force.
Local activists have demonstrated for months, protesting not only the Boyd shooting, but other shootings by city police officers since 2010.
Records show that 26 civilians have been shot, a dozen of them fatally, by city police since 2010. Before Monday, no officer had been charged in connection with any shootings.
The Justice Department in April 2014 found that "there is reason to believe" the city's Police Department had a "pattern and practice" of excessive force
. The city has since agreed to a memorandum of understanding allowing the Department of Justice to monitor the department.