In 1939, she married Marcel Leibovici (1904–1961), a stateless Romanian Jew, pianist and composer at the Folies Bergère. During the Second World War, they had two sons: Patrick (1939) and Francis (1941). Following the German occupation of Paris in 1940, Kelly, now pregnant with Francis, was arrested by the French police and interned in Besançon. She was freed from custody by the Irish chargé d'affaires, Count O'Kelly. However, in 1942, Marcel was arrested and deported to the internment camp of Gurs. The French Resistance helped him flee from Gurs and return to Paris, where he was hidden by his wife opposite the Prefecture of Police building until the Liberation. During this time, Kelly ensured him food and security at the risk of her life. Suspected of protecting her husband, she was interrogated by the Gestapo, but in spite of intense questioning, Kellysucceeded in not divulging his whereabouts. François Truffaut's film "The Last Metro" is inspired by this event in the life of Margaret Kelly and her husband.