The film begins with the sentencing of Jean-Baptiste Grenouille (Ben Whishaw), a notorious murderer. Between the reading of the sentence and the execution, the story of his life is told in flashback, beginning with his abandonment at birth in a French fish market. Raised in an orphanage, Grenouille grows into a strangely detached boy with a superhuman sense of smell. After growing to maturity as a tanner's apprentice, he makes his first delivery to Paris, where he revels in the new odors. He focuses on a girl selling plums (Karoline Herfurth) and startles her with his behavior. To prevent her from crying out, he covers the girl's mouth and unintentionally suffocates her. After realizing that she is dead, he strips her body naked and smells her until the scent fades. Afterwards, Grenouille becomes haunted by the desire to recreate the plum slicing girl's scent.
Filming was originally planned to begin in the third quarter of 2004 but the filmmakers had trouble finding the right actor to play the protagonist Grenouille. The search to find an actor to play Grenouille took nearly a year. On casting agent Michelle Guish's advice, Tykwer went to see Ben Whishaw perform as Hamlet in Trevor Nunn's production of the play. Tykwer immediately felt that he had found the actor for the role. An audition followed which convinced Eichinger of Whishaw's potential as well. Eichinger described Whishaw as embodying both "the innocent angel and the murderer." Regarding his search to find an actor, Tykwer said "it only really seemed plausible to choose someone for this role who was completely unknown. You could also say a 'nobody' who is to become a 'somebody' - because that's what the story is about too."
One of the main challenges of making the film was to convey the smells and the world of scents that Grenouille experiences. Tykwer said that to him Perfume"was much more a film about the importance of smell in our life than a film that tries to be smelly." The filmmakers strived to convey smell visually without the use of colors or special effects, Griebe says "people see the fish market full of raw, bloody fish, and they know it stinks; they see a field of lavender and know it smells wonderful. We show Grenouille taking in smells by cupping his nose, and by doing close shots of his nose, and that's it!"
Principal photography began on July 12, 2005 and concluded on October 16, 2005. The first 15 days was spent entirely on the largest stage of Bavaria Film Studios in Munich, shooting the scenes between Baldini and Grenouille in the former's workshop. All of the scenes with Hoffman were completed within the first eleven days. Most of the remaining scenes were shot in Spain, specifically in Barcelona, Girona and Figueres. The streets of Barcelona stood in for that of Paris. El Gòtic, Barcelona's historic town center, was converted into a Paris fish market. The Poble Espanyol, an open-air museum in Barcelona, was the location for the climatic orgy scene. To create an authentic dirty look, the film's crew included a "dirt unit" of about 60 people whose job was to distribute detritus over the city. Two and a half tons of fish and one ton of meat was dispersed over El Gòtic. Several mountain and forest scenes were shot in the environs of Girona. The city also provided the location of the home and studio of Madame Arnulfi. Sant Ferran Castle in Figueres provided the location for the tannery, the Paris city gates and the dungeon which Grenouille is imprisoned in. The cave in which Grenouille discovers he has no scent was also located in Figueres. Some landscape shots, including those used as Grasse's lavender fields, were filmed in Provence, France in late June 2005, before principal photography started.
