Historians including Rachel McDermott, Leonard A. Gordon, Ainslie Embree, Frances Pritchett and Dennis Dalton state that Savarkar promoted an anti-Muslim form of Hindu nationalism. Scholar Vinayak Chaturvedi states that Savarkar was known for his anti-Muslim writings.

Savarkar saw Muslims in the Indian police and military to be "potential traitors". He advocated that India reduce the number of Muslims in the military, police and public service and ban Muslims from owning or working in munitions factories.
Savarkar criticized Gandhi for being concerned about Indian Muslims. Chaturvedi notes that there was a "shift" in Savakar's views: in his earlier writings he argued for "Indian independence from British rule", whereas in later writings he focused on "Hindu independence from Christians and Muslims". In his 1907 "Indian War of Independence", Savarkar includes Muslims as heroes. This was omitted in his later writings; his 1925 "Hindu-pad-paatshahi" included Hindu heroes but not Muslim ones. In his 1963 "Six Glorious Epochs", Savarkar says Muslims and Christians wanted to "destroy" Hinduism.

In the 1940s, the two-nation theory was supported by Muhammad Ali Jinnah and Savarkar. While Jinnah supported a separate country for Muslims as a part of this theory, Savarkar wanted both religions in the same country where the Muslims lived in a subordinate position to the Hindus. Since then, RSS continued pursuing this unequal citizenship.

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