After the death of Helene, Sam van Deventer is appointed chairman of the Kröller-Müller Foundation in January 1940, on Anton’s recommendation. The administrative body still has a significant role within the Rijksmuseum, certainly as long as there is no new director. In the everyday operation of the museum, ‘assistant’ Willy Auping oversees things. He has been giving guided tours and lectures on location since the opening. He also replies to the mail and is responsible for promotion and publications, such as the Gids door het Rijksmuseum Kröller-Müller (Guidebook for the Rijksmuseum Kröller-Müller) which is published in 1939.

Apart from Auping, the staff consists of two cleaners, a porter and the caretaker Van den Brink, who lives with his wife in the museum’s staff accommodation.

The German attack on the Netherlands begins on 10 May. On that day, Sam is in Rotterdam at that time and Anton is in The Hague. Initially, little information is available, except that there is heavy fighting around the Veluwe. Sam tries in vain to contact Auping. After some time, they hear that the German troops to the north and south of the park have ‘rolled’ westward on the public roads. From the Ministry of Education, Arts and Science, which is now under German supervision, they obtain the required papers to travel by car to the museum, where they are finally relieved to find that the art collection remains untouched in the museum building. St. Hubertus is also undamaged. Sam moves into one of the five staff houses on the north side of the park and takes over the management of the park and museum. Anton is staying in hunting lodge St. Hubertus. Since the start of the war, Auping has been sleeping in the museum as a precaution. Together with Mr and Mrs Van den Brink, they are present day and night.

Initially it seems that little will actually change for the museum. Van Deventer wants to keep the museum open to the public as long as possible, so even Auping’s guided tours continue for another two months. However, paintings that do not fit within the ideas of the Nazis, so-called 'entartete art', are stored away just to be safe. For example, Le Chahut by Georges Seurat, the French cubists and the abstract work of Mondriaan and Van der Leck are removed from the wall. Instead, Auping opts for works by Dirk Nijland and the drawings of the 'Grand Museum' by Van de Velde. On the other hand, he leaves Van Gogh's paintings hanging. Auping remains committed to bringing the museum to the public’s attention. Accordingly, shortly after the invasion, in June 1940, the new catalogue of the Van Gogh collection is published and receives much attention from the press. And in the framework of the 50^th anniversary of Van Gogh’s death, on 25 June he gives a lecture for the A.V.R.O., which is also broadcast in the Dutch East Indies later that year.

A part of the collection is housed in a ‘bombproof repository for art treasures’ specially constructed by the Government Buildings Agency (Rijksgebouwendienst). The works of art are packed and brought with trucks to this bomb shelter and the cellars of hunting lodge St. Hubertus within a week. On 29 July, the bomb shelter is sealed by the National Archivist and the museum closes its doors. Auping says later: ‘we had to protect our great masters under two metres of concrete and eight metres of sand. I was embarrassed every time I closed the heavy vault doors behind me’. National Conservator Jan Cornelis Traas maintains the condition of the collection and carries out a number of conservation tasks, such as cleaning paintings and relining work.

In addition to the collection of Rijksmuseum Kröller-Müller, other valuables are also housed in the shelter, such as the treasures from the Eusebius Church in Arnhem and various objects from private collections. Even with a volume of 210m3, the space in the bomb shelter is insufficient, so part of the collection is stored in the cellars of St. Hubertus Hunting Lodge.

In the ensuing period, Sam and Anton make every effort to protect the estate and the possessions as much as possible. Aided by the old business network of Müller & Co, they are able to achieve a great deal, particularly with high-ranking German officials. When the German occupier shows interest in 3 old German masters, including Venus with Amor the honey thief by Lucas Cranach the Elder, Sam and Anton seize the opportunity to considerably improve the park and museum’s financial situation and reinforce its position. In the negotiations, they manage to get the support of Reichskommissar Arthur Seyss-Inquart. Part of the agreement is recorded in a ‘Secret report’. Sam van Deventer is appointed director of the museum by order of the occupier.