Prosecutors say Orlando Vilchez Lazo, an undocumented immigrant from Peru, picked up the victims from nightclubs and bars before the alleged rapes.
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Court documents explain that the attacks spanned five years dating back to November 2013.
In two instances, the Lazo picked up women outside Temple Nightclub on Howard Street. He threatened most of the victims with a knife, according to court records.
Lazo entered his plea in front of a judge and family members, including his wife, who declined to speak on camera. Instead, she directed media to speak with Lazo's lawyer.
"He's maintained his innocence and the Constitution entitles him to a presumption of innocence until his day in court," public defender Sandy Feinland said.
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Feinland added that his client should be tried in court and not by the media.
In response, Alex Bastian of the District Attorney's Office said that "Rape is one of the most horrific crimes imaginable that we have in our criminal justice system, and in this case, we have four victims."
Lyft said it is now beefing up its security checks. A new process will be applicable to both new and current drivers.
Lyft also maintains Lazo fraudulently represented himself to become a driver.