The gameplay in Etrian Mystery Dungeon is centered around exploring randomly generated tile-based floors in dungeons. Every action the player takes, such as movement or attacking, will trigger an action from all enemies on the floor. The goal is to find the stairs on each floor and progress through the dungeon. This game introduces a new twist with multiple sets of stairs per floor that lead to divergent paths. Additionally, F.O.E.s from Etrian Odyssey make appearances as D.O.E.s, which move between floors as they progress towards the surface.
The player's main camp is the town of Aslarga, which requires protection from the monsters that roam the dungeons. Building forts and keeping watch for these enemies are crucial to its survival. As players progress through the various dungeons, they will encounter stronger enemies, new materials, and equipment, bringing their guild closer to uncovering the mystery of Yggdrasil's dungeons.