In the wake of Pietro Badoglio's declaration of a cessation of hostilities with the Allied on 8 September 1943, Toaff and his family were forced to go into hiding, as Germany invaded Italy. He shut the synagogue when German troops arrived, an event coinciding with Yom Kippur that year, and, with the help of the Anconians, hid the members of the community in local houses and in parish churches. The adolescents and children were put on a boat sailing south to the area under the control of the Allies. The Nazis and their remaining fascist allies in Italy reacted to the armistice by organizing the first deportations for concentration camps and Arbeitslager. Toaff had been tipped off by the local parish priest that an attempt would be made to assassinate him, and he, together with his father, his wife Lia Luperini and their son Ariel Toaff, managed to take refuge in Versilia, thanks to the hospitality of the parish priest, don Francalanci. Toaff did not have the option of fleeing Italy, mindful of his father's words that: 'A rabbi does not have the same freedom of choice others have; he can never abandon his community.' He recalled later every Jew in Ancona survived the war thanks to the assistance given by their Catholic neighbours. Toaff was captured by the SS during a raid, and was saved from being executed as others had been who were caught in the roundup, when the Austrian, with whom he had conversed a little in French, and who was in charge of the execution, gave an order to release him as he was digging his own grave. Catholic families helped them throughout their flight, which led them to a refuge also in Città di Castello where, in 1999, he was accorded their honorary citizenship. Toaff himself joined the Italian Resistance in the mountains of central Italy, working also to secure the safety of fellow Jews. His company was the first to enter the village after the SS executed the Sant'Anna di Stazzema massacre, in which 560 villagers were murdered. He recalled coming across a woman who appeared to be asleep but, on closer inspection, had been disemboweled, with her fetus nearby, ripped from the womb, and shot through the head.