After several more ships, von Müller was promoted to Oberleutnant zur See, posted to the small cruiser (gunboat) Schwalbe. During the gunboat's deployment to German East Africa von Müller caught malaria which troubled him his whole life thereafter. He returned to Germany in 1900, served ashore for a time before becoming second gunnery officer of the battleship Kaiser Wilhelm II. His big break came when he was appointed to the staff of Admiral Prinz Heinrich von Preussen, where he was rated highly by his superiors. He was promoted to the rank of Korvettenkapitän in December 1908, and assigned to the Reichs-Marine-Amt in Berlin where he was noticed and praised by Admiral von Tirpitz.
von Müller was rewarded with a sea-going command: the light cruiser Emden in the Spring of 1913. He achieved fame and notice in both German and all the imperial powers' newspapers for his energy and skill in shelling rebellious forts at Nanking (Nanjing) along the Yangtse, and was awarded the Order of the Royal Crown Third Class with Swords. The outbreak of the Great War found Emden at the German base at Tsingtao. She departed there in the evening of 31 July 1914. On 4 August she intercepted and captured the Russian mail steamer Ryazan, the first prize taken by the Kaiserliche Marine in the Great War. The Emden then rendezvoused with Admiral Graf von Spee's squadron at Pagan in the Marianas.
During a conference von Müller proposed that one light cruiser of the squadron be dertached to raid Allied commerce in the Indian Ocean while the remainder of Graf von Spee's force continued east across the Pacific. Kapitän von Müller and Emden were given the assignment. Over the course of the next 12 weeks the Emden under von Müller achieved a reputation for both daring and chivalry that no other German ship has ever equalled. While taking fourteen prizes, the only merchant sailors killed by the Emden's guns were victims of a shore bombardment of British oil tanks at the port of Madras, India. Kapitän von Müller had taken precautions so that the line of fire would miss any civilian areas of the city. Emden also sank the Russian cruiser Zhemchug and the French destroyer Mousquet during a raid on Penang, Malaya. When the Emden was finally cornered by the Australian light cruiser HMAS Sydney and defeated, von Müller survived and was made captive, and with the rest of his surviving captured crew, taken to Malta. (A detachment of the crew, ashore, was missed and escaped to Germany under the leadership of Kurt von Mücke, the Emden's first officer.) However, on 8 October 1916, two days after the German resumption of unrestricted submarine warfare, he was separated from the rest of the Emden prisoners and taken to England. He escaped once, for a few hours, in 1917. The climate of England disagreed with his malaria, and he was eventually sent to the Netherlands in 1918 for treatment and as part of a humanitarian prisoner exchange. He was repatriated to Germany in October 1918.
After some considerable controversy, von Müller was awarded the Pour le Merite and finally promoted to Kapitän zur See. He retired from the Navy early in 1919 on health grounds, and setttled in Blankenburg. He was too modest to write
a book giving his account of his service. He was elected to the Brunswick provincial parliament on an anti-class platform as a German National party member, and died suddenly there, probably burnt out by frequent malarial episodes, on 11 March 1923. His other major concern of the last years was the welfare of the surviving Emden crew members.