Rune Factory 5 offers the player to play as a member of a peacekeeping group called SEED. The main character needs to defend his own community, fighting monsters and bosses. The corporation will send the user to perform special secret missions. The action will unfold in unique places inhabited by monsters and other unknown creatures capable of tearing a person apart in an instant.

The gameplay will require upgrading the farm, developing relationships with secondary characters, and solving puzzles. Many plot elements revolve around mystical runes, which contain many secrets and clues to them. It all begins with a story about the border town of Rigbart, where paranormal phenomena occur again, but on a larger scale than before. These moments affect the energy of the runes, which is why the central character is sent there to carry out an operation.

As the game progresses, the protagonist and his friends unlock access to more powerful abilities, equipment, and combat talents. In addition to adventures and constant battles, the gamer can go to the ward's new house to relax, enjoy the calm music and atmosphere. Choices in the gameplay affect the further narrative and determine what the ending will be.