The party began a coalition with the Bharatiya Janata Party (BJP) for seats in the Lok Sabha and the Maharashtra Assembly in 1989. The two formed a government in Maharashtra between 1995 and 1999.[29] The Sena was the opposition party in the state along with the BJP from 1999 to 2014.

In January 2018, Shiv Sena officially cut ties with the BJP and their NDA coalition ahead of the 2019 Indian general election after nearly 30 years of campaigning alongside the BJP. But in February 2019, BJP and Shiv Sena again announced alliance for the general elections as well as the 2019 Maharashtra Legislative Assembly election.

Shri Eknath Shinde, a senior Shiv Sena leader, wanted to reestablish the previous BJP-Shiv Sena an alliance and rebelled afterward, while gaining the majority support from the Sena MLAs.

On 29 June 2022, Uddhav Thackeray resigned from the post of Chief Minister as well as MLC member after the Supreme Court ruled that he must prove his majority. Eknath Shinde took oath as the new Chief Minister with Devendra Fadnavis as Deputy CM on June 30.

In July 2023, Shri Ajit Pawar, along with many of his supporters, left the Sharad Pawar-led NCP and joined the ruling Shiv Sena-BJP government as a Deputy Chief Minister of Maharashtra. This caused the NCP to split into two factions, with Ajit Pawar claiming in a letter to the Election Commission that he had been elected party president on June 30. In his first meeting after the split, he expressed a desire to retain the party's symbol and name, urged Sharad Pawar to retire and give opportunities to new people, and criticized many of Sharad's decisions, including the formation of a government with the Shiv Sena instead of the BJP in 2019. On 7 February 2024, The Election Commission Of India (ECI) awarded the party name and symbol to the faction headed by Ajit Pawar.

Now Together BJP, Shiv Sena, and NCP jointly run Mahayuti in Maharashtra

Jai Hind Jai Maharashtra