Daniel Chase McKibben, 36, is accused of killing Heidi Green, 59, in a home in the 5000 block of Niagara Avenue near the OB Pier on May 1.
A family member called police asking for a welfare check on her and police found her deceased. A Special Weapons and Tactics (SWAT) unit evacuated some residents nearby as a precaution.
McKibben turned up at a home in La Mesa the next day. A resident there called La Mesa Police, saying McKibben would not leave and was trespassing in the 7900 block of Rainey Street.
Police showed up at 9:15 a.m. May 2 and discovered that McKibben allegedly was armed with a knife. An officer shot him twice in the shoulder and hand.
McKibben was taken to a hospital while in custody and still remains there, a prosecutor said on Tuesday. He was arraigned in his hospital bed by a judge and the murder charge is the only one filed against him.
The prosecutor said the facts of the case were not discussed at the hospital arraignment where he was represented by a public defender.
Two hearings this week were set in San Diego Superior Court, but McKibben missed both of them because he remained hospitalized.
A status conference has been set for May 23, and future hearing dates will be set then, the prosecutor said. He remains in custody without bail and is in stable condition.