Rune Factory combines farming and life simulation gameplay with RPG elements such as real-time combat and levelling-up skills and attributes. For every one real-world second, one in-game minute passes. The player can grow crops, using upgradeable farm equipment. If a monster is tamed, it can help the player in battle, produce goods, or help to tend the crops. The player is given a limited amount of stamina, in the form of "Rune Points", or "RP". Rune Points get depleted as the player performs tasks at the farm or fights using a weapon or magic. The player is given hit points as well. If the player runs out of HP while working on their farm, they will collapse and be rescued; however, in Rune Factory and Rune Factory 2, dying outside the town causes game over. In all other games, the player will not die while fighting in the caves or ruins.
In addition to their open-ended gameplay, the games possess a linear storyline, which can be furthered by exploring dungeons and defeating certain monsters. The main character's relationship with the other villagers increases by talking to them or performing actions that please them, like giving items they like as presents for example. Some of them can even be married if their relationship improves enough. Some games of the series require the protagonist to get married as part of the storyline.