 Serving with the Eighth Army, Wheeler was present in North Africa when the Axis armies pushed the Allies back to El Alamein. He was also part of the Allied counter-push, taking part in the Second Battle of El Alamein and the advance on Axis-held Tripoli. On the way he became concerned that the archaeological sites of North Africa were being threatened both by the fighting and the occupying forces. After the British secured control of Libya, Wheeler visited Tripoli and Leptis Magna, where he found that Roman remains had been damaged and vandalised by British troops; he brought about reforms to prevent this, lecturing to the troops on the importance of preserving archaeology, making many monuments out-of-bounds, and ensuring that the Royal Air Force changed its plans to construct a radar station in the midst of a Roman settlement. Aware that the British were planning to invade and occupy the Italian island of Sicily, he insisted that measures be introduced to preserve the historic and archaeological monuments on the island.
