The Muslim Council of Britain (MCB) has elected Dr Muhammad Abdul Bari as its new general secretary at its annual meeting in London.
Mr Bari has been the deputy secretary of the MCB for four years
He was chosen from a field of 37 candidates to succeed Sir Iqbal Sacranie, the post holder since 2002.
Mr Bari, a 52-year-old Bangladeshi, is a specialist teacher in behaviour support for Tower Hamlets Council.
A central working committee will also be elected, as well as deputy general secretary and treasurer, for 2006-08.
Delegates from all the major MCB national and regional bodies are attending the meetings, as well as representatives from mosques and Islamic centres.
Mr Bari told the BBC he faced many challenges in the role.
"One of which is the deprivation, the social alienation of the whole community," he said.
"Also the elements of extremism and radicalism in a tiny section of the community. And of course the wider society - islamophobia, racism, xenophobia."
Iqbal Sacranie was knighted in the Queen's Birthday Honours in summer 2005.
He was involved in a variety of groups which culminated in the formation of the Muslim Council of Britain (MCB) in 1997, an umbrella body drawing support from hundreds of affiliates.
During his time at the helm he has been an influential voice for Muslims within 10 Downing Street and at the Home Office.
Within his own community, however, he has faced challenges to his authority over the organisation's approach to the war in Iraq, its ability to speak for younger generations and its closeness to Whitehall.