It emerged Tuesday the Conservative Party politician wrote in 2007 that the rise of the religion in the Middle East was a hindrance to the region's development.
"There must be something about Islam that indeed helps to explain why there was no rise of the bourgeoisie, no liberal capitalism and therefore no spread of democracy in the Muslim world," he wrote in an essay unearthed by the Guardian.
In the essay, titled 'And Then Came the Muslims', he also claimed "Muslim grievance" played a role in most if not all global conflicts.
"[The further the Muslim world has] fallen behind, the more bitterness and confusion there has been, to the point where virtually every global flashpoint you can think of – from Bosnia to Palestine to Iraq to Kashmir – involves some sense of Muslim grievance," he wrote.
"It is time to get deep down and dirty and examine the central charge made by everyone from Winston Churchill to the Pope, namely that the real problem with the Islamic world is Islam."
The Muslim Council of Britain hit back at the politician, telling the Guardian, "we of course are of the view that Islam has a role to play in progress and prosperity, be that in the Muslim world or here at our home in the west".
Johnson's comments have also attracted widespread criticism on social media.
The former foreign minister and ex-London mayor, has a history of inflammatory comments towards the faith.
Last year he said burqas were "ridiculous" and made women look like letter boxes and bank robbers, prompting an outcry from other politicians and British Muslim groups.
He has emerged as odds-on favorite to succeed Theresa May, who is stepping down this month after failing to get her EU divorce deal through parliament.
Some 160,000 paying members of the ruling Conservative Party are choosing between Johnson or current foreign minister Jeremy Hunt to lead the party and the country.
The winner of the mail-in ballot will be announced on July 23. The new prime minister formally assumes office the following day.