Elfir "Elie" Traum
The main protagonist. Elie is a girl from a small village who enrolls in the alchemy academy of Salburg after being saved by Marie, the protagonist of the previous game. She's punctual and generally a reliable person, but she often ends up breaking things when flustered. She has a passion for sweets, especially cheesecakes, which she has a notorious pickiness for.
One of the royal knights of Salburg. He has a somewhat brash personality, but is serious about his duty as a knight.
An alchemist from an aristocrat family, and Hermia's prized student. She has a competitive attitude towards Elie. She is in love with Nordis Fuba, Elie's classmate. However, in contrast to Nordis, she believes that any means of development for alchemy is good, even if the research could be used for weapons or other dangers. Her goal in alchemy is to make a lot of money.
The Commanding Officer of the Royal Guard.
Hallesch SleimanAn adventurer available for hire. Since Atelier Marie, he has fallen in love with Flea Schenk, though her father doesn't approve of him.
Julika JederThe daughter of a fisherman, and lover of the sea. She is integral to Elie's quest to meet Marie, as she helps her defeat the sea serpent blocking the sea route to Kentonis.
MarieAfter the events of Atelier Marie, Marie has become one of the greatest alchemists that the country has known. She has traveled far and wide to get a better understanding of alchemy, and continues to improve her abilities day by day. Prior the start of the game, she cures Atelier Elie's main protagonist Elie of a deadly illness that has been plaguing the kingdom. When Marie leaves, she travels back to Salburg, unaware that Elie is now in her pursuit.
Millcassee FrobelA nun at the Frobel church, who dislikes her current life where every day is the same. She harbors jealousy for other people with more exciting lives, but is scared of going out into the outside world. Eventually, with Elie's help, she might overcome her fears and offer to accompany Elie outside town.
My SextansAn exotic female adventurer who hails from lands south of Salburg.
Nordis FubaA gifted student at the Salburg Academy. He is very kind and doesn't want to cause any harm. However, he is prone to go into depressions when others do better than him in school.
Romauge BremerA dancer from the south. Her exotic style and dark skin resembles My Sextans, who is also from a southern country. She can be found dancing at taverns. Her dream is to live a happy family life.
Ruven FilnirA wandering adventurer for hire, still searching for his parents.
Bord LxThe owner of the Inn run in the port city of Kastagne. Originally a sailor, Bord decided to keep his Inn near the port where he could be near the ocean.
Bredolf SchigsalThe prince of Schigsal.
Bukiya no Oyaji / GerhardThe blacksmith.
ChourouThe leader of the fairies.
Dio SchenkThe owner of Salburg's tavern, the "Hasty Hideaway".
DornierThe headmaster of the Salburg Academy.
Flea SchenkDio's daughter, and the bar manager of the tavern.
A teacher at the Salburg Academy. She has been gone adventuring for nearly ten years, but has now returned to Salburg. She often butts heads with her co worker and childhood rival Ingrid, with whom she competes to see who can raise the best alchemy student (Elie VS Eisel). Hermina has a bit of an interest in the dark side of alchemy, which differs from most other's teaching methods.
- Recurring Character: She appears in Elie, Lilie, Judie, Marie & Elie, Marie Elie & Anis and her own title Hermina and Culus: Atelier Lilie Another Story, giving her an impressive record of six nearly-consecutive appearances between 1998 and 2003.
IngridAn instructor at the Salburg Academy, now teaching Elie and Nordis. She gives Elie Marie's old workshop, with the same intentions that she had for Marie.
Kreis KuhlA Meister Rank student.
- Demoted to Extra: Kreis is one of the supporting characters in Marie's character events, but isn't playable, unlike in Atelier Marie.
Kugel SchenkAlso known as Kugel Richter, the former knight. He has now joined the family business, and works at the tavern with his brother and niece.
- Demoted to Extra: He is not a recruitable party member like he was in Atelier Marie.
Luise LawrenciumThe new worker at the shop located in the academy. She may bestow Elie with various requests, and sometimes she will accidentally give a gold coin rather than a silver one as change.
Otto HolbeinThe owner of the General Store in Kasutanye. He is a sailor, and a lover of the sea. Because his store is located on the port, Otto also takes part in fishing.
Schia DonnerstageMarie's childhood friend. 6 years after the events of Atelier Marie, Schia's family has rose to multimillionare status. Schia found a talent for textiles and has new found success with her talents. Her family has become a topic of discussion around Salburg.
- Demoted to Extra: She is not a recruitable party member like she was in Atelier Marie.