In command of 2nd U.S. Dragoons, he defeated the Jicarilla Apache in Ojo Caliente, New Mexico, in 1854, was in the 1855 Battle of Ash Hollow against the Sioux, and was sent to keep the peace in Bleeding Kansas in 1856–1857.

Acquainted with Brigham Young, Cooke took part in the Utah expedition of 1857–1858, after which he was promoted to colonel and assigned command of the 2nd U.S. Dragoons.

As they prepared to ride into their first battles, they had the potential opportunity to learn from the two-volume manual on cavalry tactics written by Cooke in 1858, but not published until 1862.

It was a controversial work at the time and the War Department chose not to make it the basis for official doctrine.

Cooke espoused the value of mounted attacks as the primary purpose for cavalry forces; others, more sensibly, realized that the emergence of the rifled musket as an infantry weapon made the classic cavalry charge essentially obsolete and recommended a mission emphasis on reconnaissance and screening.

A prominent theory of cavalry charges at the time, endorsed by future generals Henry W. Halleck and George B. McClellan, was that the cavalry should be deployed in double ranks (a regiment would deploy in two lines of five companies each), which would increase the shock effect of the charge by providing an immediate follow-up attack.

Cooke ordered an ill-fated charge of the 5th U.S. Cavalry at Gaines' Mill during the Seven Days Battles, sacrificing nearly an entire regiment of regulars.

One proximate reason was the embarrassment he suffered when his son-in-law, J. E. B. Stuart, humiliated the Union cavalry by completely circling the Army of the Potomac in his celebrated raid.

Cooke served on boards of court-martial, commanded the District of Baton Rouge, and was superintendent of Army recruiting for the Adjutant General's office.

Cooke is the author of a variety of memoirs of his service: Notes of a Military Reconnaissance, from Fort Leavenworth, in Missouri, to San Diego, in California (1848), Scenes and Adventures in the Army: or, Romance of Military Life (1857), Cavalry Tactics (1862), Handy Book for United States Cavalry (1863), and The Conquest of New Mexico and California (1878).