Putnik was rehabilitated following the coup d'etat against Alexander I Obrenović in 1903. Under the new king of Serbia, Peter I Karadjordjević, he was promoted to the rank of general and appointed as the Chief of the General Staff. He then proceeded to reorganize the Serbian army by retiring old and promoting new officers, and updating outdated war plans. Putnik was Serbian Minister of War three times: 1904, 1906-1908, 1912. Putnik appointed General Živojin Mišić as his deputy. Despite occasional personality clashes, the two men had deep respect for each other. Putnik was the first officer to be appointed to the highest rank of Field Marshal. In 1912, he led the Serbian Army into spectacular victories in the First Balkan War against the Ottomans (Battle of Kumanovo, October 1912, Battle of Monastir, November 1912) and the Second Balkan War against Bulgaria (Battle of Bregalnica 1913). Field-Marshal Putnik, expecting Bulgarian attack, had deployed his troops on the most important strategic points near the river Bregalnica (Bregalnitza), which was essential for a quick victory after the sudden, unannounced Bulgarian attack.