Koi to Senkyo to Chocolate follows the protagonist Oojima Yuuki, 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 Sumiyoshi Chisato. The members leisurely spend their time in the club not participating in many activities.

When the election of the next student council president comes up, the front runner, Shinonome Satsuki, proposes that clubs with no merit should be separated and subsequently abolished. The food research club, in an act of desperation, seeks advice from the current student council president, Mori Yakumo, 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.