Nelke & the Legendary Alchemists: Ateliers of the New World invites players to fill the shoes of Nelke von Lestamm, a young noblewoman fascinated by the ancient legend of the Sage of Granzweit; which is said to bestow great power onto those who discover the mysterious Granzweit Tree. After hearing a rumor that the Granzweit Tree might lie within her father's lands near the small village of Westwald, Nelke begs her father to search for it. Her father only grants her permission on one condition – that she becomes governor of the area and develops Westwald into a prosperous city.

As Nelke works hard to enhance the lands of Westwald, she will need to call upon the help of the many alchemists that settle in the town – including those from the Atelier Marie, Atelier Elie, Atelier Lilie, Atelier Iris, Mana-Khemia, Arland, Dusk, and Mysterious sub-series. Throughout the week players will have to choose if they will spend their time on gathering resources, creating sellable items, or developing their town further; but on the weekends, they will be able to enjoy their days off building their relationships with the many charismatic alchemist residents.