A compendium of source material confirms that Stein may have been able to save her life and sustain her lifestyle through the protection of powerful Vichy government official Bernard Faÿ. Stein had met Faÿ in 1926, and he became her "dearest friend during her life", according to Alice B. Toklas. Faÿ had been the primary translator of Stein's work into French and subsequently masterminded her 1933–34 US book tour, which gave Stein celebrity status and proved to be a highly successful promotion of her memoir, The Autobiography of Alice B. Toklas. Faÿ's influence was instrumental in avoiding Nazi confiscation of Stein's historically significant and monetarily valuable collection of artwork, which throughout the war years was housed in Stein's Paris rue Christine apartment, under locked safeguard.

Although Jewish, Stein collaborated with Vichy France, a regime that deported more than 75,000 Jews to Nazi concentration camps, of whom only three percent survived the Holocaust.

In an essay written for the Atlantic Monthly in November 1940, Stein wrote about her decision not to leave France: "it would be awfully uncomfortable and I am fussy about my food." Stein continued to praise Pétain after the war ended, this at a time when Pétain had been sentenced to death by a French court for treason.

During Faÿ's tenure with the Vichy regime, 989 Freemasons were sent to concentration camps, where 549 were shot. In addition, about 3,000 lost their jobs. All Freemasons were required by law to declare themselves to authorities. In 1943 Faÿ produced the film Forces Occultes, directed by Jean Mamy, which depicts a worldwide Jewish-Freemason conspiracy.

Despite his anti-Semitism, Faÿ, who was suspected to be a Gestapo agent for much of the occupation, protected Gertrude Stein and Alice B. Toklas. Following the liberation, Stein wrote a letter on Faÿ's behalf when he was tried as a collaborator. In 1946 a French court condemned him to dégradation nationale and forced labor for life, but he managed to escape to Switzerland in 1951, funding to facilitate his prison breakout coming from Alice B. Toklas.