Police needed to disperse group chanting anti-EU slogans attempting "citizens' arrest" of Khan.
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The 133-year-old Fabian Society's New Year Conference has been disrupted just before the London mayor Sadiq Khan was due to speak, on gender equality.
Members of a group calling themselves The White Pendragons halted proceedings for several minutes, shouting "No EU", claiming the Society, a left-wing think-tank, was "subverting our English constitution".
They claimed to be attempting a "citizens' arrest" of the mayor for treason.
"It is a pleasure to be here even though we were distracted by the actions of what some would call 'very stable geniuses,' said Khan once the protesters had been cleared, referring to a Donald Trump tweet.
The small group also expressed support for Donald Trump, but many in the audience booed and cheered when police intervened to remove the protesters, and a counter-demonstration of remainers took the floor.
Some may have been angered at Khan's tweet just hours before, following the news President Trump would not be visiting Britain any time soon after all. Khan and Trump have been sparring on Twitter ever since Trump misquoted him and implied he was complacent about the risk of terror attacks in London.
Outside some protesters told journalists they also refused to recognise Khan's legitimacy as mayor because of his muslim religion.