Mizuki Usami is a passionate member of her school's art club, but the club has a problem—Usami is the only member who takes her craft seriously! The lazy club president constantly sleeps through activities and Collette hasn't regularly attended club activities in quite some time. Uchimaki Subaru, despite being an exceptional artist who could win an award if he tried, is obsessed with drawing the perfect 2D wife. Light-hearted and comedic in tone, Kono Bijutsubu ni wa Mondai ga Aru! follows Usami as she struggles to do art club-like activities, often obstructed by her motley crew of good-for-nothings and her distracting crush on Subaru.

Chihaya Ayase is obsessed with developing her school's competitive karuta club, nursing daunting ambitions like winning the national team championship at the Omi Jingu and becoming the Queen, the best female karuta player in Japan—and in extension, the world. As their second year of high school rolls around, Chihaya and her fellow teammates must recruit new members, train their minds and bodies alike, and battle the formidable opponents that stand in their way to the championship title. Meanwhile, Chihaya's childhood friend, Arata Wataya, the prodigy who introduced her to karuta, rediscovers his lost love for the old card game.

Serial murders have recently plagued Inaba, with the police struggling to find any leads. Despite this, due to his parents going abroad for work, Yuu Narukami moves to the small town to live with his uncle for a year. He enrolls at Yasogami High School, where he meets and befriends Yousuke Hanamura, Chie Satonaka, and Yukiko Amagi. While hanging out together after school, the group fills Yuu in on the urban legend known as the Midnight Channel—a mysterious TV channel that only appears at midnight on rainy days while the viewer is alone. Curious about the claim, Yuu decides to tune in that night, only to see the next victim of the serial murders appear on the screen instead. He also finds himself being drawn into the TV, which intrigues his newfound friends enough to want to investigate. Yuu ends up falling into the world within the TV, which is blanketed by a thick fog and swarming with hostile creatures known as Shadows. Realizing that this world is somehow connected to the murders, the Investigation Team forms with the goal of uncovering the mystery behind the incidents.

Starting his new term at Tanenashi High School, an unmotivated freshman searches for a club that requires minimal participation to suit his needs. He then comes across the magic clubroom, and inside is a cute upperclassman practicing her magic tricks. Suffering from stage fright that causes her to slip up in her acts, she has a tendency to end up in the most embarrassing situations. Despite having little interest in a club run by an incapable magician, the freshman finds himself involved as a new member, experiencing all sorts of awkward moments with his eccentric mentor.