MANTO throws light on the four decisive years of the life of Saadat Hasan Manto (Nawazuddin Siddiqui), a rebellious writer. The story begins in 1946 in Bombay, India. Manto is a non-practicing Muslim but has his apprehensions when the communal riots break out at a time when the country is at the cusp of freedom. He is married to Safia (Rasika Dugal) and he earns his living by writing for films. His close friends are fellow liberal writer Ismat Chugtai (Rajshri Deshpande) and film actor Shyam Chadda (Tahir Raj Bhasin).
Meanwhile, India gains Independence on August 15, 1947. Saifa goes to Lahore to attend her sister's wedding. Manto meets Shyam's family who have run from Rawalpindi to India and have lost a family member while escaping.
Shyam, in a fit of rage, expresses his hatred for Muslims and even tells Manto that he could have killed him too. A distraught Manto decides to leave India permanently and settle in Lahore. There, he is slapped with obscenity charges over his story 'Thanda Gosht'. What happens next forms the rest of the film.