Löhr succeeded General der Pioniere Walter Kuntze as Commander-in-Chief of the 12th Army on 3 July 1942. He was appointed the Wehrmacht Commander in southeast Europe on 1 August 1942, and from 28 December 1942 this position was re-designated as Commander-in-chief in southeast Europe. The forces under his command were also designated as Army Group E, and he was appointed as its commander. In this role, Löhr controlled all subordinate commands in southeast Europe, including the commanding general in Serbia (Paul Bader), the military commander in the Salonika-Aegean area, the military commander in southern Greece, the commander of Crete, the naval commander in the Aegean Sea, the German plenipotentiary general in the Independent State of Croatia, the commanding general of German troops in Croatia, and the military attaché in Sofia, Bulgaria. Löhr organised the fourth and fifth offensives against Yugoslav Partisans in 1943, during which most of those taken prisoner, including the wounded, were murdered on the spot. As Commander-in-Chief of Army Group E, Löhr oversaw the Dodecanese campaign. On 26 August 1944, with the Allies driving on Germany on three fronts, Hitler ordered Löhr to begin evacuating Army Group E from Greece and move north to defend the Fatherland.