Atelier Rorona has four main modes of gameplay: a field map, a battle screen, an alchemy system, and a visual novel system. Navigation occurs via two static map illustrations, which depicts the Arland town and its surrounding area in a scaled down view. Field map areas such as the town and forests are depicted as realistically rendered environments, in which the player can converse with locals, gather items, or encounter enemies. Enemies on field maps are openly visible to the players, and players can either engage or avoid the encounter. Contact with the enemies initiates a separate battle screen.
Battles in Atelier Rorona are turn-based and continue until either side is defeated or flees. The player may use physical attacks, items, or skills to either wound targets or heal characters. Each character and enemy has a number of hit points which depletes as he or she is attacked or performs certain skills. When a character loses all hit points, he or she faints; if all of the player's characters fall in battle, he or she is sent back to the game's town. Certain items and skills also affect the battle's element, which, depending on the element, could either increase or decrease the efficiency of certain skills performed or make additional skills available.
Atelier Rorona's storyline is presented as a series of twelve tasks. Each of these tasks amounts to three months of the game's storyline and requires the player to complete it by the end of the period. If the player fails to complete the task, the game ends and must be restored from a previously saved game. The plot develops as the player progresses through text conversations akin to a visual novel-style gameplay. Gameplay in this segment requires little player interaction as most of the duration is spent reading the text that appears on the screen. There are fourteen main plot lines that the player will have the chance to experience. To view all of the plot lines, the player will need to replay the game multiple times and perform different quests for the game's various characters.
The game opens with a brief introduction to the city of Arland, a city that is slowly being industrialized, but also a city that uses technology possessed by an ancient civilization. We are then introduced to the main character, Rorolina Frixell (Rorona, for short), who is forced to work for a master alchemist to pay off a debt her parents owe. One day, Sterkenburg Cranach (Sterk, for short), a knight of Arland, comes to the alchemy workshop and informs Rorona that the shop will be shut down unless she is able to prove that it can function in the city's economy. Over the next three years, she must pass 12 examinations to assess the ability of the workshop to do this.