Lilje was general secretary of the German Student Christian Movement 1924-34. He was involved in Confessing Church struggle in Nazi Germany from 1933 onwards. After World War II he became the bishop of the Evangelical Lutheran State Church of Hanover in 1947 until his retirement. He was also the presiding bishop of the United Evangelical Lutheran Church of Germany 1955-69, president of the Lutheran World Federation and World Council of Churches. He was also abbot of Loccum under title Johannes XI.