Amu Hinamori is a shy girl who struggles to make friends in part due to the rumors spread around school about her cool and spicy personality. Wishing that she could show everyone her would-be self, Amu wakes up to the presence of three colorful and ornately decorated eggs in her bed. Each of these Hearts Eggs houses a Guardian Character—manifestations of someone's would-be self and their dreams. With the aid of Ran, Miki, and Su, Amu now finds herself able to express who she truly is. However, things do not always pan out in her favor. The sudden appearance of Amu's Guardian Characters prompts the Seiyo Elementary Guardians, a student council-like group with each member possessing their own Guardian Character, to take notice of her. As someone who has multiple Characters, Amu is roped into being the Guardians' Joker, tasked with helping them find X Eggs—corrupted versions of one's Hearts Egg. As she becomes entangled in the Guardians' quest, Amu begins to uncover more about these mysterious Characters, the X Eggs, and the organization that seems to be at the center of it all.

In present times, Gods and Demons coexist together with Humans after the door between each of these worlds had opened. Tsuchimi Rin is a normal young high school student attending Verbena Academy, spending his days living peacefully with his childhood friend Kaede. Unexpectedly, one day the King of Gods, the King of Demons and their families move into be Rin's next door neighbors. Apparently the daughter of the Gods, Sia, and the daughter of the demons, Nerine, are both deeply in love with Rin after having met him in the past. Along with his playful friendship with upperclassmen Asa and his encounter with the silent but cute Primula, Rin has much on his hands dealing with the affections of each of these girls. Based on the eroge by Navel.

Yuugo Hachiken is studious, hard-working, and tired of trying to live up to expectations he just cannot meet. With the ushering in of a brand new school year, he decides to enroll in Ooezo Agricultural High School, a boarding school located in the Hokkaido countryside, as a means to escape from the stress brought upon by his parents. Initially convinced that he would do well at this institution, Hachiken is quickly proven wrong by his talented classmates, individuals who have been living on farms their entire lives and know just about everything when it comes to food, vegetables, and even the physiology of livestock! Whether it be waking up at five in the morning for strenuous labor or to take care of farm animals, Hachiken is a complete amateur when it comes to the harsh agricultural life. Gin no Saji follows the comedic story of a young student as he tries to fit into a completely new environment, meeting many unique people along the way. As he struggles to appreciate his surroundings, Hachiken hopes to discover his dreams, so that he may lead a fulfilling life on his own terms.

Now accustomed to his life at Ooezo Agricultural High School, Yuugo Hachiken explores the deeper aspects of what school life really means. As Hachiken learns more about himself and earns the skills necessary for his everyday tasks, he is even offered the position of the Equestrian Club's vice-president. The new semester brings a variety of agricultural dilemmas and personal conflicts, but, nevertheless, Hachiken perseveres in order to discover his dream and continue working together with his friends.