Yee, 65, entered the plea before U.S. Magistrate Maria-Elena James through his defense attorney, James Lassart, and said nothing during the hearing.
James ordered him to return to court together with 28 other defendants on Aug. 7 for a status conference before U.S. District Judge Charles Breyer, the trial judge assigned to the case.
Outside of court, Lassart and Yee declined to comment.
Yee, a Democrat, represented half of San Francisco and most of San Mateo County. He was suspended from office by the Senate on March 28, two days after the FBI arrested him on corruption and gun trafficking charges in an earlier criminal complaint.
On March 27, Yee withdrew his candidacy for secretary of state.
The superseding indictment against Yee and the other defendants was filed by a federal grand jury July 24 and replaces a previous indictment issued April 1.
In a new charge, the indictment accuses Yee and former San Francisco school board president Keith Jackson of conspiring in a two-person racketeering enterprise in which they allegedly solicited bribes and campaign contributions in exchange for political favors by Yee.
The racketeering also allegedly included a never-completed plot by Yee, Jackson and Daly City dentist Wilson Lim to import guns from the Philippines.
The charge of racketeering, defined as conducting an ongoing criminal enterprise, carries a possible maximum sentence of 20 years if Yee is convicted.
Yee is also now charged with 10 individual counts of conspiring to obtain bribes, conspiring to deprive citizens of his honest services, using telephone and text messages in the alleged honest-services fraud, and conspiring to traffic in firearms.
He is free on a $500,000 bond while awaiting the not-yet-scheduled trial.
The revised indictment contains a total of 228 counts against the 29 defendants.
In a second racketeering charge, Chinatown fraternal association leader Raymond "Shrimp Boy" Chow and 16 others are accused of conducting a separate organized crime enterprise.
That enterprise allegedly included selling drugs and guns, money laundering, gun sales, schemes to buy stolen property and a murder-for-hire plot that was never carried out.
Chow, who was previously convicted of racketeering and gun trafficking, was arraigned before James on Wednesday. He is being held without bail.
The charges against Yee include new allegations that he sought or accepted bribes to support laws to extend the term of the California State Athletic Commission and to limit the ability of out-of-state professional athletes to collect workers' compensation in California.
They also include previous claims that he accepted bribes to support medical marijuana legislation, arrange a Senate proclamation honoring Chow's association, the Chee Kung Tong, and intervene with a state agency on behalf of a software company seeking a grant.