The art collection at the Museum zu Allerheiligen includes mainly Swiss art from the late Middle Ages to the present day. In figures, the art collection includes around 2,200 paintings and 400 sculptures. The collection is due to long years of co-operation between the city of Schaffhausen, which is responsible for the museum, with foundations, art associations and private individuals. No fewer than ten institutions are still making their contributions today, such as the Sturzenegger-Stiftung, the Kunstverein Schaffhausen, the Vereinigung Schaffhauser Kunstfreunde or the Peyersche Tobias Stimmer-Stiftung. In addition, numerous loans from private individuals enrich the collection.

Outstanding works by Lucas Cranach the Elder, Tobias Stimmer, Thomas Schmid and Bernhard Strigel provide an insight into early 16th century art. The late 18th century is represented by paintings by Johann Heinrich Füssli and Johann Jakob Schalch as well as by neo-classical sculptures by Alexander Trippel, a native of Schaffhausen. Further, the collection also includes landscape paintings by important 19th century artists, such as Barthélemy Menn, Alexander Calame, Adolf Stäbli, Hans Thoma, Albert Welti and Robert Zünd.

Art of Classical Modernism is a special highlight of the collection, with prominent work groups by Cuno Amiet, Hans Brühlmann, Adolf Dietrich, Otto Dix, Ferdinand Hodler, Niklaus Stoecklin and Félix Vallotton. Over the years, the Sturzenegger-Stiftung, founded in 1987, gave the art collection the opportunity to extend these groups purposefully and substantially. Besides Hermann Knecht, Werner Schaad and Hans Sturzenegger, the work by Max Gubler is highly represented in the collection.

The second half of the 20th century is represented by works by Helen Dahm, Fischli/Weiss, Dieter Krieg, Wilfrid Moser, Roman Signer, Matias Spescha, Varlin or Ilse Weber. Furthermore, contemporary art is one of the collection's other main focuses. Works by important Swiss artists can be purchased with the funds of the city of Schaffhausen, the Kunstverein Schaffhausen and the Vereinigung Schaffhauser Kunstfreunde. Examples for important acquisitions of the last years are works by Reto Boller, Olaf Breuning, Maya Bringolf, Klodin Erb, Daniela Keiser, Renée Levi, Rémy Markowitsch, Anna Meyer, Claudio Moser, Yves Netzhammer, Léopold Rabus, Christoph Schreiber, Christine Streuli and Uwe Wittwer.