Following the outbreak of the Second World War, Kippenberger was appointed to command the 20th Battalion. He led the battalion for two years, through the Battles of Greece and Crete as well as part of the North African Campaign before being promoted to brigadier and taking command of the 5th Infantry Brigade. The pinnacle of his military career was as commander of the 2nd New Zealand Division during the Italian Campaign. He was wounded on 3 March 1944 during the Battle of Monte Cassino when he stepped on a land mine. As a result of his wounds, he lost both of his feet. After recovery in England, during which he was fitted with artificial limbs, he helped prepare for and assisted in the repatriation of newly released New Zealand prisoners of war. In 1946, he was appointed Editor-in-Chief of New Zealand's largest-ever publishing project, the "Official History of New Zealand in the Second World War 1939–45". He was still working on the project when he died on 5 May 1957 in Wellington.