After World War II he became the bishop of the Evangelical Lutheran State Church of Hanover in 1947 until his retirement.
Following WWII Lilje authored "The Valley of the Shadow" about his experiences during his imprisonment by the Nazis.
He was at Dachau concentration camp before being transferred to Buchenwald where he was held in solitary confinement.
He was tortured to extract a confession as well as reveal names of other clergy who were working to rid Germany of Hitler.
In 1964, Lilje consecrated Stefano Moshi, first presiding bishop of the Evangelical Lutheran Church in Tanzania.