The suspended senator entered his plea in federal court to one count of conspiracy to traffic in firearms without a license and illegally import firearms; one count of conspiring to defraud citizens of honest services; and six counts of engaging in a scheme to defraud citizens of honest services.
Yee is accused of selling political influence for cash and conspiring to introduce an undercover FBI agent to a Philippine arms dealer for campaign contributions.
The San Francisco Democrat is free on $500,000 bond, signing over his home on Tuesday as collateral for bond.
Yee was arrested during an FBI sting on March 26 along with several other suspects, including Raymond "Shrimp Boy" Chow, the leader of the Chinatown organization the FBI says is a front for organized crime, and Keith Jackson, Yee's campaign consultant.
About 29 suspects from the sting were indicted last week. Most, including Yee, were ordered back to court on Friday.
The Associated Press contributed to this report.