MediaGuardian.co.uk can reveal that the plot, which will hit screens in mid-June, will see Syed Masood, a Muslim property developer with a girlfriend who arrived in Albert Square six weeks ago, fall for openly gay Christian Clarke. The pair will share an on-screen kiss.
The BBC has billed the storyline as a "traditional love affair, albeit with a modern multicultural twist".
The BBC1 soap's production team researched the plot, which is bound to prove controversial with some viewers, contacting academics, gay Muslim support groups and members of the Muslim Council of Great Britain.
In the storyline, the 24-year-old Masood, played by Marc Elliott, finds his "religion and sexual feelings in conflict".
The character is currently dating Amira Shah as well as trying to work his way back into his family's good books following his flight after losing money from the family business.
Diederick Santer, the EastEnders executive producer, said: "We've always tried to make EastEnders reflect modern life in multicultural Britain and we've always told social issue stories relevant to our diverse audience.
"This isn't a moral tale of right or wrong; it's very much a human interest story where a young man struggles with the conflict between his faith and his feelings.
"In this regard, it's not dissimilar to the story we told when Dot Cotton's deeply held Christian beliefs came into conflict with her desire to alleviate Ethel's suffering [in a euthanasia plotline]."
"To all intents and purposes, Syed's a 'good' Muslim man: he doesn't drink, smoke or engage in sex before marriage. But he struggles with his sexuality when he finds himself drawn to Christian and he believes this goes against his faith.
"This is not a story about Syed and Christian's physical relationship – we don't see anything beyond one kiss. It's more about the inner turmoil and conflict Syed endures trying to remain true to his faith while questioning his sexuality.
"Syed has already been ostracised from his family and community once and if he's true to his heart he risks losing his family again."
The Masood family was introduced in 2007 following criticism that a previous Asian family, the Ferreiras, were not authentic. The intention was to develop the Masoods as "rounded human beings tackling the issues of day-to-day life in Albert Square", Santer said.
"The dynamics of Muslim relationships and families are not radically different from any others but the importance that Muslim culture places on family and married life can make the same issues more charged." [Story continued here]