Torn between his faith in Catholism and his homosexuality, Jouandeau first attempted suicide in 1914. He married the former dancer Élizabeth Toulemont in 1929, who hoped to divert his attention from the male sex; however, she was unsuccessful and Jouandeau wrote frankly about his lifelong homosexuality in Chronique d'une passion (1949).
Jouandeau was also an antisemite and his Le Péril juif is a collection of his anti-Jewish writings. In 1941 he published an article about his admiration for Germany in the NRF, which was at the time under the antisemitic wing of Drieu la Rochelle, who of course killed himself after the Liberation. The paedophile Roger Peyrefitte makes references to Jouandeau as 'Marcel Jouvenceau', to which Jouandeau objected.
Jouandeau lived in Rueil-Malmaison from 1960 until his death.