Otis took command of the Eighth Army Corps, replacing Merritt who had assumed the position of a military governor of the Philippines. Otis continued in this position during the Philippine-American War. In the Battle of Manila in 1899, he led the US Army and during the first phase of the battle before the conflict turned into guerilla warfare.

Otis was unpopular in the Philippines because of his authoritarian and “pompous” manner. His own subordinates accused him of committing abuses during the early phase of the war. However, he proved to be a skilled and able administrator. In 1900, Otis was relieved of command and replaced with Arthur MacArthur Jr., the father of Douglas MacArthur.