In many areas of Belkhyde, life is measured from war to war. Decades of conflict between the royal empire and the resistance has crippled the lands. In the world of Belkhyde, Mana and alchemists exist only in legends and folktales. Eden, the legendary land of Mana floats high in the heavens. Away from humans, both Mana and alchemists live in peace and harmony.

The lands of Eden and Belkhyde were once united in harmony until the time of the great catastrophe. Eden, a land of Mana and alchemists, distanced itself from Belkhyde, fearing contact with the humans and monsters there will lead to their destruction. All is well until Chaos resorts to the legendary power of alchemy to save his sister. Now two orphans, Felt and Viese must save Eden from crumbling. Felt transports to Belkhyde with the power of his azoth. It is up to Felt to stop Chaos' mad quest, while Viese struggles to protect Eden from further destruction.

• The story events set the setting and explain your mission. The initial goal of the game is to save Eden from destruction.
• In the beginning of the game, Viese is the only alchemist who can create valuable Mana items. Therefore, you are required to switch your characters between Felt and Viese to synthesize items.
• Travel between destinations is conducted on a simple map. Simply point and click the destination you wish to go.
• Improving upon the cost turn battle system of Atelier Iris 1, Atelier Iris 2 adopts a whole new active time battle system. Fight your way through to save Eden from destruction.
• The world of Iris is powered by spirits called Mana. There are wood Mana, flower Mana, lightning Mana, and others. Characters can work with Mana to create items and special spells to use during the quest.
• Elemental extraction is an ancient art of alchemy used to collect natural elements required for wielding items and spells. Both Felt and Viese can extract elements by destroying objects found in dungeons and action maps.
• Item synthesis is a Mana skill to create new items from objects you collect during the quest. Items you create can be used to blacksmith new weapons during the quest. The more items you create, the more weapons you can blacksmith.
• Atelier Iris 2 uses the "Action Cost Time Battle System" charging you different amounts of time for each action. The "ACTB" bar indicates character sequences. Those who are closer to the right will move first. The farther you are from the right edge, the longer it takes for your turn to move.
• Character action turns are represented on the Action Cost Time Battle bar. The closer your character is to the right end, the quicker you move. If a character is "knocked" into the orange bar on the left by enemy attacks, the character becomes vulnerable to multiple chain attacks for extra damage.
• Once a character is in break mode they are open to enemy chain attacks. Any attack during break mode adds on as a hit. The more hits you make, the more damage you do. Your own characters are also open to enemy break attacks, so be careful when your character icon is near the break zone.
• In order to use the special skills of your characters, you must fill your charge meter. The charge meter is located on the top right hand of the battle screen. Every time your character attacks or gets hit the meter charges. The number represented on the meter is the number of skills you can use. However, some special skills require more than one charge.
• Charge your power to pull off spectacular special moves. Special skills range from attack moves to healing moves.
• In Atelier Iris 2 players will be controlling two main characters. In the world of Belkhyde you will control Felt for battles and in Eden you will control Viese to support Felt with Mana items.