Heilig Landstichting was able to remain open during the war because German citizen Baader was secretary of the board. He turned out to be a fanatical member of the NSDAP, sympathised with the German occupiers and maintained close contact with the Sichterheitsdienst (SD) in Nijmegen. In 1936, German nuns took over the Casa Nova pilgrimage house from the Belgian nuns. The German nuns remained politically neutral as much as possible during the war but helped those in hiding out of charity. Boys from the neighbourhood went into hiding there, and land was made freely available for the villagers to grow their own potatoes and vegetables.

Heilig Landstichting was able to remain open during the war because German citizen Baader was secretary of the board. He turned out to be a fanatical member of the NSDAP, sympathised with the German occupiers and maintained close contact with the Sichterheitsdienst (SD) in Nijmegen. In 1936, German nuns took over the Casa Nova pilgrimage house from the Belgian nuns. The German nuns remained politically neutral as much as possible during the war but helped those in hiding out of charity. Boys from the neighbourhood went into hiding there, and land was made freely available for the villagers to grow their own potatoes and vegetables.

The quiet life at Heilig Landstichting changed overnight with the dropping of thousands of paratroopers from the 82nd Airborne Division in Groesbeek on Sunday, 17 September 1944, marking the start of Operation Market Garden. The Americans moved into the area, and Baader fled back to Germany the same Sunday. Many residents from the centre of Nijmegen fled to Heilig Landstichting during the battles for the bridges across the river Waal, quickly overwhelming the pilgrimage house. The nuns were unable to handle the stream of refugees. In addition to people in hiding, including Jews and refugees, they also provided shelter to schoolchildren.

On 2 October 1944, a barrage of shells rained down on the Heilig Lang Stichting from the Reichswald. The Court of Olives, the Palace of Pilates, Restaurant Jerusalem, the basement and front door of the monastery, and the children's chapel were hit. Many objects were destroyed, including old Palestinian pottery and a collection of old Palestinian coins. A shell punched through the dome of the Cenacle Church. Prioress sister Bernharda, who had been staying at St. Canisius Hospital for some time, was arrested on suspicion of espionage. The nuns were no longer allowed any contact with the outside world, and on 7 November, they received notice that they had to leave. It was not until 4 September 1945 that the Military Authority in Tilburg allowed them to return to Casa Nova. Peace returned to Heilig Landstichting after 8 February 1945. A total of 34 war victims are buried at the Heilig Landstichting cemetery.