Waheed Kesmatyer, 24, is suspected of fatally stabbing Jack Baker, 67, in the 1000 block of Bush Street, police said.
Police found Baker when they responded to a request for a well-being check at the home at about 6:15 p.m. on Feb. 11.
Physical evidence at the scene was linked to Kesmatyer, who had been roommates with Baker since October 2010, police said.
Kesmatyer was already being held in Marin County Jail on unrelated charges when he was served with the arrest warrant for murder.
Police and prosecutors were not yet releasing what the motive might have been for the killing.
During his arraignment in San Francisco Superior Court today, Judge Nancy Davis read the charging document, which stated that the murder happened sometime between Feb. 6 and Feb. 11, the date Baker was found dead.
Kesmatyer pleaded not guilty to a charge of murder with an enhancement for the use of a deadly weapon, the knife allegedly used to stab Baker.
Kesmatyer's arraignment had initially been scheduled for last Friday and again on Tuesday, but had been postponed both times due to mental health issues.
He is due back in court again on April 7 to set a date for the preliminary hearing.