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.

Souta meets Mahiru, who suffers from Androphobia, the fear of men. The rest of the staff sets them up to share shifts in a suicidal, for Souta at least, attempt to cure Mahiru.

Yachiyo the samurai sword carrying waitress reveals that she started carrying it to ward off bullies back in elementary school. At this time she encounters Kyoko who agrees to act as a body guard in exchange for Yachiyo's lunch. Otou Hyougo, the true restaurant manager, returns to the store after another unsuccessful search for his lost wife. His wife who has the worlds worst sense of direction got lost years ago while out shopping.

Takanashi is visited at work by one his 4 sisters. Hiroomi the assistant cook attempts to blackmail the staff of Wagnaria so that he won't have to work. At the same time it becomes apparent that Satou the head cook has a thing for Yachiyo the head waitress.

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.

Takanashi spends some quality time with his four quirky sisters; the boss, the drunk, the writer and the manipulative. Each in their own way is reliant on Takanashi to keep their family in order. White Day has arrived and Takanashi gifts Mahiru a bag of hair pins. This is the first White Day gift she has ever received. Later he runs into her on the street worried that she might attack some random male while walking around he escorts her home. On the way they run into his eldest sister Kazue. Mahiru get flustered and admits to "assaulting" Takanashi on a regular basis.

Otoo returns to Wagnaria once again this time bringing with him a new waitress, Yamada Aoi. Aoi tells a "tragic tale of woe" to which Takanashi responds that she is a liar. Reluctantly he ends up training Aoi in how to be a waitress. As the day progress she tries to assign the various staff members into a fake family structure.

The girls decided to take a trip to the hot springs which will be the first time for Mahiru. Takanashi concerned about the fate of the male guests at the hot springs goes as well. In the end the entire staff ends up going only to be so late that the hot spring is closed by the time they arrive.

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.

Kyouko is gone for a week on company business and in her absence Yachiyo attempts to "serve" Jun, which results in his heart being crushed even more. Later Nazuna sees Takanashi and Mahiru walking home together and bribes Kyouko to let her work at the restaurant for the day to spy on Mahiru. Mahiru eventually admits that she likes Takanashi, though Nazuna misinterprets this thinking that she was confirming that Takanashi was a masochist.

Yamada tells a scary ghost story at the end of work and Mahiru is to scared to go home where she would be by herself. Takanashi invites her over to spend the night at his house, Yamada follows them there, claiming to be too scared even though she was the one who told the story in the first place.

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.

Popura becomes upset with Sota constantly calling her small. Later, Sota becomes devastated when Kyoko kills a bug, inadvertently insulting Popura and Inami in the process.

Aoi becomes curious about Hiroomi's secret life and drags Popura into stalking him, despite the fact he is completely aware of it. Later, Popura tries to get Sota to treat Mahiru nicer. Tired of Jun's teasing, Popura tries to get revenge on him which does not go to plan. Meanwhile, Aoi acts very clingy around Otoo after he comes back from his recent trip.

Sōta's novelist sister Izumi enters a slump when she assumes he is dating Popura and will stop paying attention to her. She decides to go on a journey where she ends up meeting Mahiru who helps cheer her up. As Sōta looks after Izumi, Nazuna helps out at Wagnaria, which annoys Aoi who believes she is outshining her. After hearing about it, Nazuna puts on an act to make Aoi feel better about herself.

Whilst out shopping for some more cream, Kyōko and Yachiyo end up meeting Otoo's long lost wife, Haruna. As Yachiyo debates whether to tell Kyōko about her, she disappears again. As Yachiyo feels guilty about it, Mahiru learns about Jun's one-sided crush on Yachiyo and starts feeling sorry for him, leading Sōta to believe she has a crush on Jun. With some support from Jun, Yachiyo apologises to Otoo after he returns and cheers up.

Popura and the others try to think of ways to help Sōta get along better with Kyōko. Wanting to be spoiled in a similar manner to Kyōko, Aoi starts learning how to make parfaits, much to the dismay of Jun. In order to stop Kyōko from eating everything in the store, Hiyoomi tells a white lie which leaves her stunned. When Sōta finds a lost girl, Kyōko is told to look after her, and even avoids taking her food. After the girl is reunited with her mother, Jun gives Kyōko some food as thanks.

Popura and Jun end up catching colds due to Aoi's clumsiness, so Kyōko calls in two of her juniors, Yohei and Mitsuki Mashiba, twin siblings who don't get along. When Kyōko offers to put someone else in charge of looking after Inami, Sōta becomes upset and falls out with Inami, but Inami soon manages to build up the courage to make up with him.

Mahiru meets a boy calling himself Kirio Yamada, who she believes might be Aoi's brother. As he is able to withstand her punches, Mahiru ends up conversing well with Kirio, who starts developing feelings for her, but Sōta becomes downhearted when he sees the two getting along. He begins acting strangely the next day and ends up bashing his head against the wall, leading him to think he might've become a masochist. Later, Kozue manages to get the waitresses to dress up in animal cosplay.

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.

Jun takes Yachiyo to buy a cellphone, whilst Kozue takes a liking to Yohei. Meanwhile, Mitsuki becomes suspicious of Jun's familiarity with Yachiyo whilst Yamada runs away after Sōta scolds her.

Mahiru finds herself a bit too close to Sōta for comfort when he tries to stop a tower of boxes from falling on her, which leads her to become a bit fearful of him the next day. This turns into a complete freakout after she discovers Sota touching her head whilst she was asleep and stops coming into work. Later, Poplar gets locked in the freezer and initially suspects Jun, but soon finds Aoi just did it accidentally. After Mahiru doesn't show up at work all week, Sōta goes to visit her in Kotori-guise to apologise and exchange phone numbers.

Aoi searches for her teddy bear, Daisy, only to find that Jun had just put it in her room. Later, Yachiyo overhears a conversation between Jun and Mitsuki and assumes the two are going out with each other. As Jun notices her weird behaviour, he takes some advice from Popura to put some pressure on himself to sort things out with her.

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.

Souta spends the day looking after the little girl who came before, leading Popura to start feeling a little left out. The next day, Aoi comes across Haruna, seeing her as a potential mother and bringing her to Wagnaria, where the other staff try to keep her put until Otoo returns, but she somehow manages to escape regardless.

Souta is given the task of reporting his family's activities to Otouru Minegishi, Kazue's ex-husband and an employee of his mother who has an annoyingly masochistic behavior. The next day, Souta has to deal with poor eyesight after his glasses break because of Aoi punching him with Daisy. while Hiroomi tries to encourage Jun to ask Kyouko out for a drink.

Realizing that he and Yachiyo both have the same day off, Jun finally finds the courage to ask her out for drinks. Meanwhile, Yamada devises multiple plans to get Sota to pet her again.

As Kyōko remains spaced out over the previous day's events, Popura tries to act more reliable to fill in for her, while Mitsuki tests Jun to see how compatible he is with Yachiyo. Meanwhile, Sōta is bewildered over suddenly finding Mahiru to be cute, outright denying Kirio's suggestion that he might be in love with her. While trying to compliment Mahiru on how much she's improved with her anthrophobia, Sōta inadvertently upsets her by suggesting she find someone else to fall in love with.

While Sōta remains stressed over the other day's events, Izumi, assuming he had broken up with Popura, tries to set Sōta and Mahiru up with each other, unaware of the actual circumstances between them.

As Sōta feels conflicted over his feelings towards Mahiru, Aoi, wanting Hiroomi to give her some attention, tries to obtain information on the blossoming relationships. Later, Popura gets a toothache and takes the day off, having a dream where she becomes a magical girl. Meanwhile, Kirio ends up discovering Aoi, who is revealed to be the sister he was searching for, and is met with resistance when he tries to take her back home.

Staying over at Sōta's house, Aoi explains her backstory about being constantly forced to study by her mother, inevitably pointing out the reason she ran away was because Kirio ate her natto. As the other staff members try to convince Aoi to return home over the next few days, Popura asks Kirio to bring over his mother, Kikuno, who is revealed to have trouble talking with others clearly to the point that her children need a manual to understand her.

With Aoi's situation resolved, Sōta continues to be in denial over his feelings for Mahiru. Meanwhile, having finally learned Yachiyo's birthday, Jun gives her all the presents that he hadn't had the courage to give her before. Later, Aoi gets herself a cellphone, which she attempts to use to communicate with Kikuno, while Popura becomes depressed when she believes she's gotten shorter.

As Popura becomes more aware of the relationships blooming around her, she and Aoi question Otoo about the restaurant's stance on romantic relationships. Later, Minegishi comes to the restaurant to tell Sōta something and gets punched by Mahiru, leading her to feel she hasn't gotten over her androphobia, but Sōta manages to calm her down.

Jun finally works up the courage to confess to Yachiyo, but it doesn't go well and Yachiyo goes into hiding. After managing to find her, Jun gives a direct confession which she finally reciprocates. Afterwards, Kyoko seems to want to stop Yachiyo making parfaits for her, saying she shouldn't be tied down to her, but Jun accepts that Kyoko is a key part of the girl he fell in love with.

Jun finally works up the courage to confess to Yachiyo, but it doesn't go well and Yachiyo goes into hiding. After managing to find her, Jun gives a direct confession which she finally reciprocates. Afterwards, Kyoko seems to want to stop Yachiyo making parfaits for her, saying she shouldn't be tied down to her, but Jun accepts that Kyoko is a key part of the girl he fell in love with.

Still dressed as Kotori, Sōta gets some surprisingly sound love advice from Kirio, who instantly sees through his disguise. Meanwhile, Sōta and Jun become curious about how Hiroomi hasn't been snooping into people's businesses lately, only to find he has simply been more secretive about it. Later, Yachiyo tells Popura that she plans to quit Wagnaria to expand her horizons, assigning her as the next chief.

Aoi, curious about Sōta's delayed reactions, is tasked by Yachiyo with taking a photo of Hiroomi for an album. Meanwhile, as Sōta and Mahiru go on their date, they are interrupted by Mahiru's father, who Mahiru hits when he starts insulting Sōta, managing to work things out with him. Later, Yachiyo announces her resignation to the rest of the staff, with Sōta encouraging Popura to do her best as the next chief before being mysteriously abducted.