Christians on the Left says a number of Christian groups have used biased news reports and online articles to circulate "racist slurs", and to promote "Islamophobic fear" and "nonsense" about the Labour politician.
Sadiq Khan was announced early this morning as the winner of the London mayoral election and he now becomes the most senior Muslim politician in Western Europe.
Director of Christians on the Left, Andrew Flannagan, told Premier: "It's been a priviledge to help [Sadiq] get a sense of the life and depth that is pulsing through the Church.
"It's something that he's very aware of already but he's seen it in even greater measure in the last few weeks.
"The Christians that know Sadiq, many of the folk from his old ward and his constituency in Tooting happily work and know the character of the guy.
"Some of us don't have relationships with many Muslims and some of us don't have the relationships that we could but those who do have relationships with Sadiq Khan - many Christians, including myself - we're very happy to work with him and have been working with him for years.
"It shows how relationships trump fear."
Before attending an official ceremony at Southwark Cathedral to swear him in as London mayor, Sadiq Khan said: "Fear doesn't make us safer, it only makes us weaker, and the politics of fear is simply not welcome in our city."
"I grew up on a council estate... Back then, I never dreamt that someone like me could be elected as Mayor of London, and I want to say thank you to every single Londoner for making the impossible possible today."
Sadiq Khan's main rival in the mayoral election, the Conservative's Zac Goldsmith, has been criticised for branding Mr Khan a "radical" and highlighting his supposed links with Islamist extremism.
The Richmond Park MP was accused by David Cameron's former adviser, Steve Hilton, as bringing back the "nasty party label to the Tories.
The Defence Secretary Michael Fallon, who himself labelled Mr Khan a "Labour lackey who speaks alongside extremists" during the campaign, defended the tactics used by the Conservatives as "the nature of our democracy and the rough and tumble of politics."