In January 1916 she married Georges Hanna Sabbagh with whom she had two sons: Jean and Pierre. Agnes and Georges divorced in 1934.
A few days after the fall of Paris on 14 June 1940, having fled Paris to be with her mother at the house of a cousin at Vicq-sur-Breuilh, she heard an appeal on the BBC by General de Gaulle who encouraged the people of France to continue the struggle against the occupying Germans and Vichy government.
It was offensive to her when books were removed from her library and replaced with works by German authors. Then, on August 6, a notice was fixed on the gateway of the Palais de Chaillot, ordering free entry to German soldiers, and she wrote in her diary that she told her colleague Jean Cassou, "I feel I will go mad, literally, if I don't do something!" So, with Boris Vildé, Anatole Lewitsky, Jean Cassou and Yvonne Oddon she formed the Groupe du musée de l'Homme from members of the Museum. It was the first resistance movement in occupied France.
In a few months they built a highly diffuse underground network. Their action spread rapidly with the creation of a clandestine newsletter, Résistance, which had only five issues, between 15 December 1940 and the end of March 1941, with editorials holding no illusions regarding Pétain and the Vichy government. This group went on to feed information to the British.
After leaders of her Resistance cell were betrayed and arrested in April 1941, Agnes recruited Pierre Brossolette to lead the group. All of them were arrested and sent to the harsh Cherche-Midi prison before ending up at Fresnes. They were tried by the Wehrmacht in February 1942.
Agnes was then transferred to the Prison de la Santé where conditions were improved. She was visited by her mother and son Pierre who told her the men had been put to death by firing squad (in their last moments, singing "Vive la France").
The women were sentenced to five years slave labor and deported to Anrath prison in Germany. Agnes was made to work in appalling conditions at the Phrix rayon factory in Krefeld where workers died, went blind and developed horrible skin conditions. After four years, in June 1945 she was liberated by the Third United States Army.
From the fall of Paris to her first arrest and interrogation by the Gestapo in April 1941, Agnes kept a written diary. Apart from a few scribbled notes, she didn't resume writing in it until her liberation from prison in April 1945. She wrote about taking part in the Nazi Hunt at Wanfried in 1945, setting up soup kitchens for refugees (and expressly stated that everyone was to get a share, even the German civilian) and later helping to start the denazification process.
After the war, Agnes refused to return to work at the Museum. Though her health had been affected by her experiences, she continued to write books on art. She published her diary under the title Notre Guerre in 1946. This was later reissued and translated into English (by Barbara Mellor) under the title Résistance. In 1949 she was awarded the Croix de Guerre with silver gilt palm for heroism. She spent her final years with her son Pierre in the village of Valmondois and is buried in the cemetery there.