Rizzo, who is charged with more than 50 counts of fraud, had one count dropped and another added.
Rizzo's former assistant, Angela Spaccia, former Mayor Oscar Hernandez and former Councilman Luis Artiga also pleaded not guilty to corruption-related charges. The judge set a pre-trial hearing for May 3.
Spaccia, who was facing four counts of misappropriation of public funds, had four charges added: three counts of conflict of interest and one count of misappropriation of public funds.
The city of Bell has been without a functioning government since voters recalled its previous officeholders March 8. On Monday night, Gov. Jerry Brown signed emergency legislation allowing newly elected Bell City Council members to take office.
The Los Angeles County Board of Supervisors is slated to meet next Tuesday to certify the election, meaning a new Bell City Council could be sworn in by next Wednesday.
The Associated Press and City News Service contributed to this report.