Haruka Haruno, a young girl who wishes to be a princess, meets a strange boy named Kanata who encourages her dream and gives her a special charm. Several years later, Haruka enrols at the prestigious Noble Academy boarding school, where her new roommate, Yui Nanase, shows her around the campus. Whilst hiding in the woods over her embarrassment over revealing her dream, Haruka comes across Puff and Aroma, two fairy siblings from the Hope Kingdom. Just then, they are approached by Close, an emissary from the evil DysDark organization, who traps Yui's dream of becoming an author in a Gate of Desperation to create a monster known as a Zetsuborg. As Haruka becomes determined to protect Yui's dream, her charm turns into a Dress Up Key, which Haruka uses with the Princess Perfume the fairies brought with them to become the Princess Pretty Cure, Cure Flora. Using her new powers, Haruka manages to defeat the Zetsuborg and rescue Yui. Afterwards, Puff and Aroma reveal they were sent in search of the Princess Precure by Kanata, who is revealed to the Prince of the Hope Kingdom.

Puff and Aroma explain to Haruka, they got separated from Kanata after the Hope Kingdom was attacked by Dys Dark, led by a witch named Dyspear, entrusted with finding the three Princess PreCures who possess the Dress Up Keys. As Haruka decides to train hard to become a proper princess, student council president Minami Kaidou finds a Dress Up Key washed up on the beach. After observing Minami's graceful elegance, Haruka asks her to teach her how to do ballet so that she can become more princess-like. Despite the strictness of the lessons, Haruka continues to work hard, only to end up spraining her ankle whilst attempting an advanced move. While treating her injury, Minami confesses that she is far from perfect, only possessing her ballet skills from training hard as a kid, expressing her joy that someone asked her for lessons. Later, as Close targets a boy yearning to be a soccer star to create a Trophy Zetsuborg, Minami spots Haruka transforming into Cure Flora as she goes to fight against it. With Haruka's sprained ankle leaving her at a disadvantage, Minami's desire to protect her gives her the ability to transform into Cure Mermaid and defeat the Zetsuborg. Just as Haruka and Minami are about to celebrate their new partnership, Puff and Aroma discover that the third Princess Perfume in their possession has gone missing.

While Minami works with Puff and Aroma to find the missing Princess Perfume, Haruka joins the rest of the freshmen in cleaning the dorms. However, Puff gets discovered by the dorm superviser, Reiko Kisaragi, who states that pets can't be kept in the dorm. After studying the rules, which requires every student to agree in order to implement a new rule, Minami gives Haruka one week to unanimously convince the other students to let Puff stay in the dorms. Over the week, Haruka manages to use Puff's charms to convince almost everyone, with the exception of Kisaragi, who doesn't get along well with dogs. Before Haruka can think of a solution, Dys Dark's second emmissary, Shut, targets a karate practitioner to create a Karate Zetsuborg. As the PreCure fight against the Zetsuborg, Puff leads Kisaragi to safety, only to run into Close wielding his own Zetsuborg. Puff risks herself to protect Kisaragi until Haruka and Minami arrive and defeat both Zetsuborgs. Thankful for Puff's efforts, Kisaragi makes the vote to keep her magnanimous, allowing her to stay in the dorms. Meanwhile, another student in the dorms is seen with the Princess Perfume.