He was unable to secure entry to the Military Academy in Mexico City but, assisted by the influence of General Reyes, enrolled as a sergeant in the 7th Cavalry Regiment.

Shortly after enlisting, however, he deserted; he was promptly tracked down, arrested, sent to the military prison in Tlatelolco for 5½ months, and demoted to a private in the 23rd Infantry Battalion.

Upon his return from East Asia, the government of President Porfirio Díaz placed him in charge of the military garrison on Clipperton Island, an atoll in the Pacific subject to a sovereignty dispute between Mexico and France.

An American ship arrived, bringing provisions and rescuing a German, Gustav Schultz (the representative of the company which mined guano on Clipperton Island), who had lost his mind.

In 1915, an outbreak of scurvy claimed many of the colonists' lives and in 1915, by now desperate and at the head of a colony that had no food, Arnaud set sail with three soldiers in a canoe in pursuit of a passing ship they had spied.