Inspite of being a devout Muslim, Sir Syed also criticized the influence of conventional orthodoxy pertaining to religion and society that made of the Muslims in India suspicious of British influences. Sir Syed also started to feel increasingly concerned for the future of the Muslim community. Being born and brought up in an elite and posh household Sir Syed was very well aware of the best of Muslim tradition and also knew about the steady decline of the political power of Muslim across the country.
The hostility between the Muslims and British before and after the rebellion (Revolt of 1857) threatened to marginalize Muslim communities across India for many generations. He also started to whole-heartedly promote the co-operation with British authorities, promoting loyalty to the Empire amongst Indian Muslims. Sir Syed was fully committed towards upliftment of Muslims and also founded the modern madrassa in Muradabad district in 1859 - the first religious schools to impart scientific education.
Sir Syed also contributed towards societal upheaval, thus helping to organize relief for the famine struck people of North West Province in 1860. He also set up another modern school in Ghazipur in 1863.
As soon as Sir Syed transferred to Aligarh in 1864, he started to work as an educator. He also set up the Scientific Society of Aligarh, the first scientific association of its kind in Indian sub-continent. It was actually modelled after the Royal Society and the Royal Asiatic Society; Sir Syed assembled Muslim scholars from different parts of the country. The society also held annual conferences, disbursed funds for educational causes and also regularly published a journal on the scientific subjects in Urdu language and English. Sir Syed also felt that the socio-economic future of Muslims was threatened by their orthodox aversions to modern science and technology.
He also published many writing promoting liberal, rational interpretation of religion and social taboo. Sir Syed also holds the view that Jesus mentioned in Holy Quran died and there is no avenue for any new messiah and neither a messiah is needed for Muslims as Islam is a complete religion. On the pre-colonial system he said "The rule of the former emperors and rajas was neither in accordance with the Hindu nor the Prophet Mohammadan religion. It was based on nothing but tyranny and oppression; the law of might was that of right; the voice of the people was not listened to" (Bipan Chandra: India's struggle for independence).