The current mosque structure was constructed after destroying an ancient temple dedicated to Hindu goddess Kali and a sacred Hindu site.It is believed by some that Sayyid Ali Hamdani had the temple of Kali demolished and built the present mosque with its material and that a spring dedicated to Kali is still inside the mosque. The railing at the back of the mosque complex leads to a bright orange marking on the stone just below that suggests to the foundation belonging to the destructed Kali Shri temple.Local Hindus were involved in various communal disputes and repeated altercations by 1942, agitating for the right to build a covered shrine adjacent to the Muslim shrine,which eventually led to a boycott of Muslim-owned shops by Kashmiri HindusIn ‘Eminent Personalities of Kashmir’, a book edited by a Kashmiri Hindu, Krishan Lal Kalla, mentions that according to Hindu belief, Khanqah was first the Kali temple. The book claims: “When Hazrat Ameer Kabir returned from Makkah, he went into the temple and offered his prayers. After he left the place, it was found that he had left footprints on that stone plate where he had bowed before the God. That temple was converted at once into Khanqah-e-Moula.Toward the River Jhelum, there is a wall marked with Sindoor (or Sindooram, a traditional vermilion red or orange-red colored cosmetic powder from India, usually worn by married women along the parting of their hair) but not a temple and water oozes at a place, which Kashmiri Hindus say is dedicated to goddess KaliHowever, others have questioned the validity of such claims, and believe it to be a revisionist attempt to re-cast history as traditional Kashmiri Hindu historians, such as Kalhana, Jonaraja and Shuk Bhatt make no mention of the existence of any temple at the site of the structure. The counterclaim stemming from the fact that a Hindu religious site also exists adjacent to the shrine and the historians have suggested that the two sites have in fact always been adjacent to one another,their proximity being representative of communal tolerance. Kashmiri Hindus have also historically held the Khanqah in high reverence. On 15 November 2017, a fire broke out in the shrine which damaged the spire of the building. Fire tenders were brought on the scene and they managed to arrest the spread of the fire which prevented any further damage to the building. Restoration work was immediately started and on 30 March 2018, a refurbished crown was successfully installed on the spire of the shrine.[Saleem Beg, a member of INTACH, states that the holy place of Hindus and the Khanqah co-existed together.
