Takanashi Souta, lover of all things small, is recruited by his tiny sempai Taneshima Popura to work at the family style restaurant Wagnaria. There he meets his new co-workers and begins to learn about their many quirks.

Takanashi takes the day off work to take care of his sick sister. The staff attempts to function without them and deal with Mahiru's fear of men with no male server to deal with the male customers.

The source of Mahiru's fear of men is revealed to be a plan concocted her father. Mahiru's father finds out that Takanashi gave her a gift for White Day and visits the restaurant to meet him. Mahiru, afraid that he has come to make her quit working there ask Takanashi to pretend to be a girl. Takanashi mans up and wears a skirt.

Pupura finds out about Takanashis tall sisters and is upset with him for keeping these ideal women from her. As punishment she sets him up to go on a date with Mahiru. An experiment to see how much more man acclimated Mahiru has become concludes that if she can't punch Takanashi she'll kick him in the nuts.

Takanashi and Mahiru go on their "date". The staff of the restaurant fearing for Takanashi safety concoct an elaborate plan to have him cross dress so that Mahiru would think of him as a girl and not hit him. As the date comes to a close Takanashi comes to realize his true feelings for Mahiru and Mahiru receives the compliment of her life.

Sōta becomes depressed when he discovers Nazuna has grown as tall as him and has Popura act like his little sister for the day. Mahiru becomes jealous of this and works with Hiroomi to try and get Sōta to call her cute. The next day, Kirio comes to Wagnaria to look for his sister, but finds himself coming into conflict with the men, whilst Hiroomi attempts to keep him and Aoi from meeting each other.

Popura and Aoi try to help Mahiru train to cure her androphobia by dressing her up as a guy, but with no such luck. Later, Sōta and Mahiru start exchanging text messages, which causes Izumi to worry. Sōta also runs into Kirio, who manages to deduce that Mahiru has feelings for him. Later one night, Aoi gets locked out of the restaurant, but Jun manages to sort things out for her. Later, Popura and Aoi try to help out Mahiru's progress by exposing her to the other men, only for her to nearly end up punching Hiroomi. Meanwhile, Popura becomes elated when she is finally able to reach the broken items report sheet that was normally out of her reach.

Whilst Popuar is pleased to finally reach the report sheet, Sōta is horrified by the thought of her growing taller. Whilst talking about the future, Aoi ends up turning a statement from Popura that she might have to leave Wagnaria some time in the future to a rumour that she is actually quitting, which she spreads to the other staff members. As the staff have their concerns over this, much to the annoyance of Maya the bird, Popura is confused by their weird reactions to her. After Maya helps Popura with her worries, the truth about Aoi's rumour soon comes out.