He entered the Navy as a midshipman during the War of 1812, serving in the attack on Kingston, Upper Canada, in November 1812, and in the capture of York in April of the following year; and for gallantly on board the Niagara in Perry's victory on Lake Erie, September 10, 1813.

On July 9, 1846, Montgomery and his detachment from the Portsmouth raised the American flag over the plaza in the town of Yerba Buena (today's San Francisco).

At his direction, Lt. Joseph W. Revere also lowered the Bear Flag flying at Sonoma, California, north of San Francisco Bay and raised the U.S.

The lowered Bear Flag ended up in Montgomery's possession and, in 1848, he delivered it to Naval authorities in Boston.

In other action of the Mexican–American War, Montgomery blockaded Mazatlan for some months, and, with the assistance of Captain Lavalette in the Congress, captured Guaymas.