When "Emden" sent a landing party ashore to destroy a radio station at Port Refuge in the Keeling Islands on November 8, 1914, she was finally cornered by the Australian light cruiser HMAS "Sydney" and was defeated in the Battle of Cocos by the Australian ship's heavier guns. Müller, with the rest of his surviving crew, was captured and taken to Fort Verdala, Malta. A detachment of his crew which had gone ashore evaded capture and escaped to Germany under the leadership of "Emden"s first officer, Hellmuth von Mücke. On October 8, 1916, two days after the German resumption of unrestricted submarine warfare, Müller was separated from the rest of the "Emden" prisoners and taken to England, where he was interned at a prisoner of war camp for German officers located at the Midlands Agricultural and Dairy College (now the Sutton Bonington Campus of the University of Nottingham). In 1917 he led an escape of 21 prisoners through a tunnel, but was recaptured. The climate of England disagreed with his malaria, and he was eventually sent to the Netherlands for treatment, as part of a humanitarian exchange of prisoners. In October 1918, a month before the armistice, he was repatriated to Germany.