They lost their ballot status in 2020 under a change in the New York state election law that required at least 130,000 votes on the party line every two years.

[9] In the elections for Governor of New York in 1994, 1998, and 2002, the Independence Party's candidate was businessman Tom Golisano, whose personal wealth enabled him to mount well-funded campaigns.

Because Golisano received more than 50,000 votes each time, the party was guaranteed an automatic ballot line for the following four years.

In 2001, the Independence Party endorsed Michael Bloomberg, the billionaire Republican candidate for mayor of New York City.

The following year, the New York City Industrial Development Agency (with agreement by the state) approved an $8.7 million bond to help finance a new headquarters for a youth charity controlled by Newman and Lenora Fulani, Newman's chief spokesperson and a prominent Independence Party public figure.

The media characterized approval of the bond as a reward from the Mayor as well as an incentive by Governor George Pataki (see below) to obtain Newman and Fulani's support for his re-election campaign.

In May (only four days after final approval of the IDA bond), Golisano, supported by IP founder Laureen Oliver and many of the original founding members, launched a primary challenge.

In September, Golisano lost the Conservative write-in primary but won narrowly to achieve ballot listing on the Independence line.

In the primary battle and in the general election, MacKay and followers of Newman within the IP, including Fulani, supported Pataki.

In the November 2002 general election, Golisano retained row C for the Independence party by polling 14% of the popular vote.

(Golisano later changed his own party registration to Republican, but finally decided not to seek nomination to succeed retiring Governor Pataki.)

In September 2005, the brewing struggle resulted in the party's state executive committee's ousting Fulani and other Newman followers.

The catalyst was a media controversy over Fulani's refusal to publicly disavow her now-infamous 1989 statement that Jews are "mass murderers of people of color".

But Fulani—whose supporters called the purge racist, sexist, McCarthyistic and even antisemitic—continues to be active in the party's Newman-controlled New York City machine.

The New York County chairperson Cathy Stewart and party strategist Jacqueline Salit run it on Newman's behalf.

[citation needed] The New York City organization remains the most influential of the party's factions because of its small army of hard-working volunteers and the financial support it receives from prominent politicians and Newman's own political and psychotherapy base.

On February 4, 2006, the Executive Committee of the Independence Party of the State of New York dissolved the Interim County Organizations of Brooklyn, Queens and the Bronx, which had been controlled by Newman and Fulani.

The Committee's resolution stated the action was a result of the antisemitism and racism espoused by Fulani and Newman, which are antithetical to the principles of the Independence Party.

On June 4, 2006, State Chairman Frank MacKay started dis-enrollment hearings against Fred Newman, Lenora Fulani, and almost 140 of their followers, in order to seize control of the New York City county organizations.

The Nassau County committee was forcibly dissolved in February 2011 after MacKay seized control over the party's operations from Bobby Kalotee.

[36] In 2022, the Independence Party of New York attempted to regain ballot access by supporting Lee Zeldin, the Republican nominee for governor.

A petition was filed with the New York State Board of Elections, with the Republican slate seeking to restore the Independence Party line.