A small Muslim community in the prairies finally gets its own mosque–the problem is, it's in a church! Reverend Magee, who was tricked into the deal by the scheming Yasir, is suddenly very unpopular with his parishioners. The mosque's new Imam, Amaar Rashid arrives from the big city to smooth things over, but his easy charm and progressive ways do little to convince the locals that Muslims aren't simply a bunch of terrorists. A handshake deal between the new Imam and Reverend Magee ensures that Mercy's Muslims are here to stay
Baber, Mercy Mosque's conservative voice, decides a barrier must be erected to separate the men and women during prayer. Rayyan protests, convinced the community's liberal voices will prevail. But she has no idea what she's up against. A battle of the sexes ensues and Amaar's compromise ensures that no one will be happy. Meanwhile, Baber continues his long-standing and rather futile campaign to have Layla wear the hijab.
What better way to improve your image amongst suspicious townsfolk than to hold an open house at the Mercy Mosque? Amaar enlists Yasir to fix the room's decrepit electrical system before the big day arrives. Of course, the Muslims simply can't agree on what the open house should include. Long-winded history lectures? Islamic dating tips? Muslim munchies? In the end, the turnout is spectacular, but things come to sudden halt when an electrical fire has the guests convinced they're under attack.
Mercy's Muslim women protest co-ed swimming classes at the local pool. Mayor Popowicz refuses to change the rules, nervous at what voters will think if she's seen kowtowing to the Muslims. Meanwhile, Baber refuses to let Layla go out for Halloween, causing Amaar to suggest an Islamic version of the heathen holiday. In the end, the pool remains integrated, but Fatima dons an outrageous bathing suit to ensure she remains fully covered.
Marlon, a new white convert, has the entire mosque in a tizzy. Marlon's zealous embrace of Islam wins an immediate friend in Baber, but he soon alienates everyone by passing judgment on virtually everything the Muslims do. Meanwhile, Sarah, never too devout, decides it's time to become serious about Islam. But her passion soon wanes, even as Marlon's intensifies. Soon the entire mosque is cooking up hair-brained schemes to dampen Marlon's zeal.
Yasir's overbearing mother arrives from Lebanon with an exciting new proposition. Sarah is shocked to find that mother Hamoudi has plans for Yasir to take a second wife! Mayor Popowicz advises Sarah to fight back and take a second husband. Meanwhile, Reverend Magee ponders whether he should perform a gay marriage, amidst the protests of just about everyone. Yasir eventually solves his marital problems with a clever scheme that convinces his mother that one wife is enough.
When the Archdeacon announces he's coming to Mercy Anglican, Reverend Magee fears for the worst. With church attendance is way down, and the place just might get shut down. Because the Muslims realize that they have a stake in this as well, Yasir cooks up a scheme to have Muslims pose as Christians to help fill the seats. The archdeacon arrives early and quickly figures out the entire scheme, but he's delighted at the possibilities for the mosque's lucrative rent money.
Amaar searches for the perfect way to propose to Rayyan after getting Yasir's permission to marry his daughter. Sarah volunteers to help but soon what is supposed to be the most magical night ever becomes a series of comic misfires. Meanwhile, when Thorne finds the town has turned on him after his bad behavior toward the Muslims, he tries to find a new way to fit in.
Rayyan sets out to convince Amaar that they should have children some day by inviting him to help her babysit a newborn. But when the baby takes to Amaar and not to Rayyan, she's less sure she's in a hurry to become a mother. Meanwhile, Thorne recruits Sarah to help him win over Amaar as a friend but instead ends up destroying a peace offering he had made to the Imam.
Amaar becomes self-conscious about his own meager earnings compared to those of his fiancée, Rayyan, who is always eager to pick up the cheque and pay for gifts. He decides a pre-nup is the best way to show her he won't be financially dependent on her. Meanwhile, Thorne is wracked with guilt when Sarah discovers he lied to replace her in a community bridge game.
Rayyan urges Amaar to befriend a lonely Rev. Thorne but quickly finds herself shut out when the former frenemies find much in common. Meanwhile, when a mishap at the Mosque is misread as a hate crime, Sarah covers for the Mayor until she has to come clean and mend fences between the Anglicans and the Muslims.
Urged on by the women of the Mosque, Rayyan runs for the board. But her victory is short-lived when Baber finds a clause in the constitution forbidding women from participating. Worse yet, Amaar agrees to uphold the constitution, no matter how upset Rayyan is. Meanwhile, Thorne enlists Sarah to help him connect with the people of Mercy and she loses her newfound friends to him.
When Yasir announces his impending return, Amaar and Rayyan seize the opportunity of his visit to set a wedding date. They soon discover they don’t have time to plan a big wedding and turn the event over to Sarah, who goes over the top with arrangements they don't love. Amaar saves the day when he finds the perfect spot for them to marry. Meanwhile, the only way Thorne can get Baber to help with his tax problem is to convince cranky Fred to do a favour for Baber.
Having mastered his work at the mosque, Amaar has devoted himself to good works volunteering for Islamic Assistance International and is thrilled when they offer him a full-time job. But that joy is tempered with sadness when he realizes the job would take him to Montreal and that Rayyan isn't sure she wants to move. Meanwhile, Sarah and the Mayor become convinced a new doctor in town is trying to steal Rayyan's practice.
Not wanting to cast a pall over their special day, Amaar and Rayyan decide to wait until after the wedding to let their family and friends know they're moving to Montreal. But Baber overhears their juicy news and lets it slip at the worst possible moment. Everyone's shocked reaction threatens to derail the special occasion. Meanwhile, Yasir feels left out and struggles to find his role in the family and in town.
Amaar and Rayyan cut their honeymoon short and return home so that they can help Sarah deal with her divorce from Yasir. Rayyan tries to drag Sarah to a divorce support group but when Sarah won’t go Rayyan brings the group to her. Meanwhile, Amaar decides to sort out his Imam related issues with Baber and Thorne once and for all.
Rayyan is back to work at her clinic and not happy with her new receptionist, Poppy. When Amaar tries to resolve her employee problem, Rayyan’s stress level at home goes through the roof. Meanwhile, Ann takes the newly single Sarah Cunningham (her maiden-name) to Odayna for a ladies night at a local bar. When Baber and Thorne realize Sarah’s religion may be up-for-grabs, they compete to win her religious allegiance.
After blowing out the old fuse box in their house, Amaar tries to impress Rayyan by playing Mr. Handyman but has to secretly enlist Sarah’s do-it-yourself expertise to get the job done. Rayyan becomes suspicious of his sudden upsurge in Mr.-Fix-it skills and volunteers Amaar to fix Fred’s shower, Meanwhile, Baber and Thorne challenge each other to a fasting competition that escalates to insane heights, even for them.
Amaar needs Baber and Thorne’s cooperation to win a coveted Multi-Faith Award, but Baber and Thorne try to cut Amaar out when they discover the award comes with a cash prize. Meanwhile, Ann sets Sarah up on the worst first-date of her life, which leads to the worst second-date of her life. And Nate and Fatima team up to make a multi-ethnic sandwich.
Thorne’s brother Charles arrives in town to audit Ann for Revenue Canada - and reconcile with Thorne. Thorne tries to send Charles packing despite Ann’s growing attraction. Meanwhile, Amaar and Rayyan’s first official dinner party as a married couple goes off the rails when Amaar’s attempt at a fancy French recipe goes up in smoke.
Amaar is getting impatient waiting to find his new purpose when Baber sticks his nose in where it doesn’t belong, leading to an unexpected sign from above. Meanwhile, Ann’s crush on Charles fuels old sibling rivalries when she encourages her new flame to help out with Rev. Thorne’s Destination Church Spectacular. Sarah is left to deal with the town audit single-handed.
Amaar tries to get the town to support his new Mosque, but finds only disinterest and some outright derision when he reveals that his divine inspiration came from a chicken. Meanwhile, Baber is determined to prove the town isn’t ready for a new mosque by trying to get himself arrested. Sarah has a crisis of faith and considers eating bacon, while Ann suffers a crisis of love while sexting the now absent Charles Thorne.
Sarah feels undervalued by Ann and agrees to work for Darnelly’s Mayor, Glenda Beckford, not realizing that Ann’s college ‘frenemy’ has ulterior motives for hiring her. Meanwhile, Amaar is so consumed with his plans for the new Mosque, he manages to forget Rayyan’s birthday. Baber and Thorne compete for clients at the mosque/church’s last rummage sale.
When Amaar inadvertently leads everyone to believe that the new Mosque is haunted, Sarah runs damage control and suggests he and Rayyan spend the night in the Mosque to prove it’s completely ghost-free. Meanwhile, a love-struck Nate goes to extreme lengths to ask Poppy out on a date. And Thorne helps Baber overcome his irrational fear of Jinn.
In the lead up to the series finale, Amaar reveals to Baber that he plans to be the Imam of the new Mosque. In turn, Baber revolts and forms a splinter Mosque. Meanwhile, Ann is distraught over Charles’ upcoming nuptials to a younger woman and comes up with a bizarre strategy to fight for her man. And Sarah attempts to rejoin the church choir, with fiery results.
In a series finale that lets Little Mosque on the Prairie live up to it’s namesake, Amaar prepares for the grand opening of the new Mosque, while trying to get Baber to end his boycott. Charles returns to Mercy with a plan to win Ann. Sarah reaffirms her Muslim faith; and, with Mercy Anglican burnt to a crisp, Thorne finds an unexpected new home for his congregation.