Sam van Deventer takes a variety of measures to protect the museum and the art collection. The threat of aerial bombardment is particularly concerning. For this reason, a white circle on a blue square is painted on top of the tower of St. Hubertus hunting lodge, making it recognizable as cultural heritage.

At the insistence of Helene, the construction of a bomb shelter in a sand dune on the Veluwe began in 1939, but is not yet finished when the war breaks out. Sam manages to get the German army to provide manpower and rolling stock to complete the work. In July it is ready. All the works of art are packed and transferred to the bomb shelter in just one week. On 29 July the shelter is sealed by the National Archivist and the museum closes its doors. The National Conservator Jan Cornelis Traas monitors the condition of the collection and carries out some conservation work.

Sam manages to arrange that Friedrich Christiansen, Wehrmachtsbefehlshaber (Army Commander) in the Netherlands, writes a letter stating that it is forbidden to besiege De Hoge Veluwe Park, to use it as a training ground or to hunt in the park. Sam hangs copies of the letter on the entrance gates and fences of the park but is unable to prevent part of the park being occupied by the German Air Force and used as a military airfield. For this too, Sam, assisted by Anton, is able to arrange a substantial compensation agreement that greatly improves the financial position of the park.

Anton feels the end approaching and on 26 August 1941 he writes to Mary Lehnkering-Bottler, Van Deventer’s future wife: ‘All my hope for the further existence of the National Park – the jewel that was left to us as the life-work of our dearly departed – is placed in Sam’s cooperation and leadership’. After his first heart attack, he tells Sam that he has burned his papers and that Sam must act as if he is no longer there. On 5 December 1941, at the age of 79, he dies in his chair in front of the window in St Hubertus hunting lodge. He is buried next to Helene on the southern slope of the Franse Berg.

Although the museum is closed, De Hoge Veluwe National Park receives 31,787 visitors during the year. A very brief annual report mentions 10,663 people who visited the hunting lodge, an increase compared to the previous year. The annual report attributes this to an apparently growing interest in the architecture and furniture of ‘Dr Berlage’. With cautious optimism, plans are made to open a part of the museum to the public in the summer months and exhibit works by Floris Verster, Jan Voerman, Henri van Daalhoff, Jan Zandleven, William Degouve de Nuncques and Théo Van Rysselberghe. Most of the works are already hanging when a bomb explodes nearby and ruins the plan. The works are immediately returned to the shelter.

As early as 1941, Sam asks the architect Henry van de Velde to think about an extension for the museum. There is no longer such a desire to build the ‘Grand Museum’, rather the idea is to add a new wing and to regard that as the final museum. Van de Velde agrees to this and designs a sculpture gallery, extra display rooms and an auditorium for openings and presentations. Unlike in the rest of the building, large windows are conceived for the sculpture gallery, an opening to the surrounding nature.

Van de Velde visits several times to discuss the plans with Van Deventer, H.P. Bremmer, Chief Government Architect Kees Bremer and the architect Gerrit Baas, who once again takes charge of the construction work. Despite the scarcity of building materials and staff, construction begins in 1943. However, in September 1944, new military operations around Arnhem bring the construction to a halt.