After Paul Klee's death on 29 June 1940 Rolf Bürgi, a Bern collector and friend of the Klees, supported Lily Klee-Stumpf, Paul Klee's widow, as asset administrator and adviser on the management of the estate.

In 1945 Lily Klee stipulated in her will that her husband's artistic estate be managed by a commission to be made up of, besides her son Felix, the Zurich art historian Carola Giedion-Welcker and the Bern collectors Werner Allenbach, Rolf Bürgi, Hans Meyer-Benteli and Hermann Rupf.

To pre-empt the threat of seizure by the Allied Powers under the Washington Convention, Hans Meyer-Benteli and Hermann Rupf purchased the artistic estate of Paul Klee from Lily Klee on 20 September through the agency of Rolf Bürgi. Lily Klee-Stumpf died two days later, on 22 September.

On 24 September 1946 Werner Allenbach, Rolf Bürgi, Hans Meyer-Benteli and Hermann Rupf founded the Klee-Gesellschaft [Klee Society] and transferred Paul Klee’s artistic estate to the Society.

On 30 September 1947 the Klee-Gesellschaft founded the Paul-Klee-Stiftung [Paul Klee Foundation]. The Foundation's assets comprised some 1,800 works. The Board of Trustees was chaired by Hermann Rupf.

In 1949 Felix Klee moved from Germany to Bern with his family at the invitation of the Klee-Gesellschaft, and laid claim to his inheritance.

In 1950 the Klee-Gesellschaft handed over a further 1,500 works to the Paul-Klee-Stiftung.

The dispute between Felix Klee and the Klee-Gesellschaft was settled out of court in 1952. The Paul-Klee-Stiftung was confirmed as of right and was able to take up its work.

The purpose of the foundation was now defined: Firstly to create an “inalienable asset to the arts” and secondly to “establish in Switzerland a facility accessible to serious scientific research”. The foundation assets comprised some 2,500 works by Paul Klee.