She and the rest of the White Rose were arrested for distributing the sixth leaflet at the University of Munich on 18 February 1943. The Scholls brought a suitcase full of leaflets to the university main building. They hurriedly dropped stacks of copies in the empty corridors for students to find when they left the lecture rooms. Leaving before the lectures had ended, the Scholls noticed that there were some left-over copies in the suitcase and decided to distribute them. Sophie flung the last remaining leaflets from the top floor down into the atrium. This spontaneous action was observed by the university maintenance man, Jakob Schmid. Hans and Sophie Scholl were taken into Gestapo custody. A draft of a seventh pamphlet, written by Christoph Probst, was found in the possession of Hans Scholl at the time of his arrest by the Gestapo. While Sophie Scholl disposed of incriminating evidence before being taken into custody, Hans tried to destroy the draft of the last leaflet by tearing it apart and trying to swallow it. The Gestapo recovered enough of it and were able to match the handwriting with other writings from Probst, which they found when they searched Hans's apartment. The main Gestapo interrogator was Robert Mohr, who initially thought Sophie was innocent. However, after Hans had confessed, Sophie assumed full responsibility in an attempt to protect other members of the White Rose.
In the People's Court before Judge Roland Freisler on 21 February 1943, Scholl was recorded as saying these words:
On 22 February 1943, Scholl, her brother, Hans, and their friend, Christoph Probst, were found guilty of treason and condemned to death. They were all beheaded by guillotine by executioner Johann Reichhart in Munich's Stadelheim Prison only a few hours later, at 17:00 hrs. The execution was supervised by Walter Roemer, the enforcement chief of the Munich district court. Prison officials, in later describing the scene, emphasized the courage with which she walked to her execution. Her last words were:
Fritz Hartnagel was evacuated from Stalingrad in January 1943, but did not return to Germany before Sophie was executed. In October 1945, he married Sophie's sister Elisabeth.