The mosque became the first formal place of Islamic worship in England. Queen Victoria's British Indian employees and her British Indian secretary, Abdul Karim, used the mosque when the Queen visited Windsor Castle. A small number of dignitaries, students, and guests used the mosque until Leitner's death in 1899, following which the mosque closed. Chapter IX of HG Wells's "War of the Worlds", published in 1898, contains a description of the Mosque being set on fire.
The mosque fell into disuse between Leitner's death and 1912. Khwaja Kamal-ud-Din, a prominent Kashmiri lawyer and founder of the Woking Muslim Mission, worked to repair and revive the mosque. Leitner's son wanted to sell the land to property developers so Khwaja took him to court on the grounds that the Mosque was consecrated ground just like a church and therefore deserved the same rights and property limitations. He won and after purchasing the grounds from Leitner's son for a small price he was able to re-open the Mosque in 1913. The mosque was managed from 1914 to the mid-1960s by members of the Lahore Ahmadiyya Movement. It attracted royal visitors and famous British converts, such as Lord Headley and Marmaduke Pickthall. The mosque became a centre of Islam in the UK. During the First World War, the incumbent imam, Sadr-Ud-Din, petitioned the UK government to grant nearby land to the mosque as a burial ground for British Indian Muslim soldiers. By 1917, this burial ground had been constructed and received the bodies of 19 soldiers from the hospital for British Indian soldiers at Brighton Pavilion. Until the arrival of Pakistani immigrants in the UK in the 1960s, the Shah Jahan Mosque was the centre of Islam in Britain. It was from the mosque that The Islamic Review was published, as well as Maulana Muhammad Ali's - popular English translations of the Quran. It has also been claimed as the location at which the name 'Pakistan' was coined. Among those that visited the mosque in this time were Faisal of Saudi Arabia, Muhammad Ali Jinnah, Haile Selassie, Mir Yousuf Ali Khan, Aga Khan III, and Tunku Abdul Rahman.
By the 1960s, the influence of the mosque had declined and was seen more as a local mosque than vital to the practice of Islam in the UK. In the 1970s, it transferred into Sunni hands and was revived as an important place of worship in the community. The mosque was badly damaged in June 2016 after floods swamped homes in the surrounding area.