During his time in office, Prajapat has frequently bucked his party, which has been the ruling party of Rajasthan since 2018. In 2021, Prajapat sided with Rajendra Singh Rathore and Gajendra Singh Shekhawat, both high-ranking members of the BJP, in calling for an official investigation into the police killing of an alleged smuggler in Barmer district. Prajapat stated that he believed that the Barmer police were not being truthful about the incident, which Prajapat described as a "planned murder".[8] Prajapat stated that he would resign from the Rajasthan Legislative Assembly if an investigation was not conducted.[9]
Throughout his career, Prajapat campaigned strongly for the creation of a new district centered around the city of Balotra. Balotra is the largest subdivision of the Barmer district, and there has been a longtime campaign to separate it from Barmer, fueled in part by the creation of a new oil refinery in the area.[2][10] In February 2022, as a result of the state government's budget proposal, which did not include a provision to create a new district for Balotra, Prajapat vowed to walk barefoot until "the day Balotra is declared a district".[11] Later at a dinner hosted by Ashok Gehlot, the chief minister of Rajasthan and a member of the INC, Prajapat rebuffed an offer by Gehlot for a pair of shoes and left the dinner without eating.[12][13]
In 2016, Prajapat was arrested at a protest in Balotra against Rajasthan State Industrial Development and Investment Corporation (RIICO), in which Prajapat allegedly slapped a RIICO regional manager. As a result of Prajapat's arrest, the other protesters began clashing with security personnel.[14] In the 2021 trial, Prajapat and 27 other protesters were acquitted of their charges.[15]