He was promoted to captain in the U.S. 4th Infantry Regiment and served in a variety of posts in the Pacific Northwest in the Washington Territory before being assigned to duty in California.

His Company E was stationed at Fort Jones in Siskiyou County, where he joined the Freemasons, becoming a member of the North Star Lodge No.

In 1854, Judah participated in an expedition against local Native Americans, but was too inebriated to lead his company in an attack on a group of Indians who were hiding in a cave.

The commissary officer, Lt. George Crook (a future Civil War general) later wrote, "It seemed that the rear guard had gotten some whiskey, and were all drunk, and scattered for at least 10 miles back.

With the outbreak of the Civil War in 1861, Judah was colonel of the 4th California Volunteers at Fort Yuma, a post on the Colorado River opposite the Arizona Territory.

Judah returned to a staff position during the winter of 1862-63, when he served as acting inspector general of the Army of the Ohio.

Judah's Indiana and Illinois cavalry under Edward H. Hobson defeated Morgan at the Battle of Buffington Island, but failed to capture the general (who finally surrendered to other Federal troops on July 26).

Judah was placed on routine administrative duty in the Department of the Cumberland until the end of the war, stationed in Marietta, Georgia.

Since no crops had been grown here on the battlefields in 1864 and, as the surrender had paralyzed the local economy and government, the citizens and former soldiers lacked food, funds and employment.

Judah, seeing that aid was needed to prevent suffering, issued corn and bacon to the needy until a crop could be harvested.