Koi to Senkyo to Chocolate follows the protagonist Yuuki Oojima, who attends Private Takafuji Academy, a large school with over 6,000 students. Yuuki is a member of the food research club, along with seven others, including his childhood friend Chisato Sumiyoshi. The members leisurely spend their time in the club not doing much activities. When the election of the next student council president comes up, the front runner Satsuki Shinonome proposes that clubs that have no merit should be sorted out and abolished. The food research club seeks advice from the current student council president Yakumo Mori, who suggests Yuuki run in the election as an opposing candidate. Yuuki learns about the issues facing the school and decides to run in the election.

The story is set on an archipelago of four islands far south of Japan or even the South Seas. It is all but a different world from modern Japan. From the discovery of anti-gravitons came the dream invention of anti-graviton shoes ("grash") that let people fly the skies. They introduce people to a new realm by enabling flight with just one's own body strength, without feathers or engines. This led to the rise of the sport of "Flying Circus" (dogfight race). The protagonist who once hoped for a future in this sport suffered a setback due to an overwhelming defeat, and withdrew from the sport for this and some other reason. However, he met the transfer student Haruka Kurashina, and in teaching her to fly the skies, the old passion returned. He takes part in the Flying Circus again. (Source: Anime News Network)

In Takafuji Academy, clubs of all kinds exist, including a Food Research Club. One day, during the student council election campaign, they find themselves a target of club disbandment under new financial reforms. They have decided to enroll into the elections. Will they be able to prevent their club from getting disbanded?