Kremsmünster Benedictine Abbey in Upper Austria, founded in 777, was seized by order of the Gestapo in 1941 and placed under the administration of Reichsgau Oberdonau (Upper Danube). From summer 1941 it was used to store artworks for the "Sonderauftrag Linz". The proposal came from Gau curator Franz Juraschek, who, like Gauleiter August Eigruber, hoped it would work in favour of his Gau and suggested that the valuable objects stored in Kremsmünster should be shown "in the form of an exhibition". Nothing came of this, but Eigruber's suggestion was heard by those responsible for the "Sonderauftrag Linz", and important items secured and seized in Vienna in 1938  and managed at the time by the Institute for Monument Preservation were transported to Kremsmünster. The first and largest transports took place in May and June 1941 (28 May, 30 May, 4 June, 11 June, 24 June, 26 June) and included paintings, prints and art objects and furniture from the Alphonse Rothschild, Louis Rothschild, Oscar Bondy and Albert Pollak collections and, to a lesser extent from the collections of David Goldmann, Rudolf Gutmann, Felix Haas, Felix Kornfeld, Wally Kulka, Alfons Thorsch, Emmy Aldor and N. Pilzer. The transports were organized by Spedition Bäuml. While the Gau leadership and monument preservation authority hoped to store the most valuable objects in Kremsmünster, Hans Posse, head of the Linz project, quickly decided that more and more items from the "Führerbau" depot in Munich considered to be inferior should be transferred to Kremsmünster so as to make space in Munich for more valuable ones. Between August 1941 and November 1943 1,732 paintings were transferred from Munich to Kremsmünster, and some of the items transported from Vienna to Kremsmünster were kept there only in temporary storage prior to onward transport to Munich (for example, a transport on 24 August 1942 of objects from the collections of Berta Morelli, Ferdinand Bloch-Bauer, Oscar Bondy, Franz Erlach and others). Until 1943 transports continued to come from Vienna, and in 1942 two transports (25 September and 24 November) with eighty-eight paintings and fifteen crates of art objects from the "Jagd" depot in Steinbach near Göstling were also transferred to Kremsmünster. According to the Benedictine father Richard Rankl, in autumn 1943 there were around 5,000 pictures and 400 crates in the Kremsmünster Reich Art Depot. They were kept in the baroque ceremonial hall (Kaisersaal) and in several rooms of the former convent. For security reasons, the doors were bricked up and moved. The art historian Justus (Heinrich) Schmidt, who was head of the art history department of the Gau museum in Linz and deputy culture officer of the Reichsgau Upper Danube, was appointed as local manager of the depot. His deputy in Kremsmünster was art historian Father Petrus (Franz) Mayrhofer. Ignaz Hager, the provisional administrator of the abbey appointed by the Linz Gestapo, also considered himself responsible for the Reich Art Depot and complained about the unclearly defined competences and responsibilities of the staff of the "Sonderauftrag Linz", the Vienna Institute for Monument Preservation and the Linz Gau offices. In spite of the camouflage measures designed to protect the abbey complex from air raids, the Kremsmünster Reich Art Depot was too unsafe in the event of aerial bombardment, and its contents began to be removed in 1943. They were transferred in part to Hohenfurth Abbey (Vyšší Brod), which had also been seized by Reichsgau Upper Danube, and to Thürnthal castle, but mostly to the salt mine in Altaussee, which was now the central depot for objects intended for the planned "Sonderauftrag Linz".

Even after the contents had been transferred to Altaussee, Kremsmünster's role as an art depot was not over, because after the war the abbey was once again used to hold artworks, this time while awaiting their return and restitution. On 6 May 1945, the US military authorities appointed the prior, Father Richard Rankl, to manage the abbey, and on 29 July 1945 the abbot was able to return. Between November 1945 and summer 1946 art objects from Austria were transferred in eight shipments from the Central Collecting Point in Munich to Kremsmünster. They included objects seized from Viennese collections and already stored in the abbey during the war, and also expropriated church property from the abbeys at Kremsmünster, St Florian, Göttweig and Klosterneuburg. According to existing lists, the items were stored this time in the abbey mill and in rooms such as the Apostle Room within the abbey itself. From 1948 the abbey urgently requested that they be removed. At the time, objects that had not yet been restituted were transferred in 1949 for temporary storage in the depot of the Federal Monuments Authority in Salzburg-Kleßheim.