Stella Deus is a story-driven tactical role-playing game in which the player controls a group of characters both picked up during the course of the story and in side events. The world is navigated using an overworld map using point-to-point navigation, with a date system showing the length of time it takes to get to a selected location. Alongside the story missions, Towns can be visited, in which characters can customize and create new weapons and armor, sell existing equipment in exchange for money, and shop for items such as healing potions. In camps set up on a journey, characters can swap out weapons and armor, equip items such as healing potions and beneficial charms for future battles. Special items used in character leveling can also be crafted by the player. Alongside story-based missions, there is a special dungeon called the Catacomb of Trials, where characters can battle and gain experience levels, raising their general statistics. The number of available levels in the Catacomb increases as players progress through the game. Each character has a specific character class, which they keep throughout the game and continue to level up as they gain experience points (XP). Higher amounts of XP are awarded for executing special abilities. Along with swordsmen and archers, there are alchemists (mages), priests (healers), and units who fight using most things from axes to fists.

Most battles are triggered based on story events, and are completed when the stated object has been accomplished by the player, be it defeating all enemies, defeating a boss, or performing a specific task. At the end of each battle, the players gain a summery of their performance and spoils gained. The game uses the turn-based Replaceable Action Position battle system, much of which was carried over from the battle system used in Hoshigami: Ruining Blue Earth. Players navigate the field across a grid-based map, which can include obstacles such as bodies of water and high structures. Character positioning within the environment can be used to their advantage, such as an archer gaining higher accuracy when at a high point in the level. Character actions are arranged in a set order, and each character's weapon dictates their attack range. Each time a character performs an action, they gain experience points and additional Skill Points (SP) that can be used to purchase supplies or raise individual character stats. Three types of Skills can be equipped for characters: Action Skills, a special attack that player execute for a certain amount of Magic Points (MP); Support Skills, which grant passive abilities such as scaling higher obstacles; and Zone Skills, which grant passive abilities to both the equipped character and those in close proximity to them.