The Suikoden manga exists in several distinct adaptations, each based on different entries in Konami's role-playing game series. The most prominent of these is the adaptation of Suikoden III, illustrated by Aki Shimizu, which spans eleven volumes.

This story is set in the Grasslands, a vast expanse of plains home to several allied clans, and the neighboring Zexen Commonwealth, a powerful nation of knights. These two factions have been locked in a bitter war for generations. The narrative is driven by three central characters from opposing sides whose fates become intertwined. Hugo is the adolescent son of the chief of the Karaya Clan, raised in the Grasslands and raised to fight against Zexen. Chris Lightfellow, known as the Silver Maiden, is a young and highly skilled captain of the Zexen Knights, haunted by the loss of her father in the conflict years ago. The third protagonist is Geddoe, the taciturn captain of a mercenary unit in the service of the Holy Harmonian Empire, a powerful theocratic state to the north whose fifty-year truce with the Grasslands is about to expire.

As Hugo is sent as an envoy to negotiate peace with the Zexen, Chris is simultaneously dispatched to the Karaya village on a similar mission of truce. However, a mysterious third party sabotages these efforts. Chris is framed for the murder of a Lizard Clan chief, forcing her to order her men to burn the Karaya village to escape. In the ensuing chaos, she kills one of Hugo's friends in self-defense, an act Hugo witnesses, igniting a burning desire for revenge. The situation escalates dramatically when the Harmonian Empire invades the Grasslands, ostensibly to recover one of the 27 True Runes, powerful magical artifacts that govern the fundamental aspects of the world. Rumors spread of the return of the legendary Flame Champion, a hero who wielded the True Fire Rune and defeated Harmonia fifty years prior. As Hugo, Chris, and Geddoe pursue their own goals, they are drawn into a widening conflict that forces complex alliances, blurring the lines between hero and villain as they unite against a common imperial enemy. The series explores themes of vengeance, duty, and the cyclical nature of war, featuring a large cast of characters that includes a cigar-smoking military duck and an army of ax-wielding rabbits.

Another manga, Gensou Suikoden: Soul Eater, is a three-volume adaptation of the first Suikoden game. It follows Tir McDohl, the son of a great general of the Scarlet Moon Empire. When his father is called away to battle, Tir begins his own career in the Imperial Army. Through his friend Ted, he comes into possession of the Soul Eater, a True Rune that governs life and death. Corrupt officials within the empire, led by the court magician Windy, ruthlessly hunt for this rune, forcing Tir and his companions to flee the capital. He soon crosses paths with a rebel organization, and after a devastating attack on their hideout, Tir is convinced to take up the cause. With the help of the former Imperial strategist Mathiu Silverberg, he builds a Liberation Army from a small band of rebels into a force powerful enough to overthrow the corrupt Scarlet Moon Empire. The earliest and rarest manga is the Konami Parody Comic Series Genso Suikoden, published before the release of Suikoden II, which features a mix of serious and humorous stories about characters from the original game, including events like Odessa Silverberg's marriage.