Delegates to the secession convention had voted in March 1861 to secede from the New Mexico Territory and the Union, and seek to join the Confederacy.

Arizona was proclaimed a Confederate territory on August 1, 1861, after Colonel John R. Baylor's victory at the Battle of Mesilla.

Since the proceedings of the Tucson convention were never ratified by the United States Congress, the Provisional Territory was not considered a legal entity.

After the start of the American Civil War, support for the Confederacy was strong in the southern part of the New Mexico Territory.

These Native Americans were attacking White settlers, killing off ranchers and mining camps all over Traditional Arizona.

On March 16 the convention adopted a secession ordinance, citing the region's common interests and geography with the Confederacy, their political sympathy with the Southern secession movement, their opposition to the "sectional" party, the "Black" Republicans, the need of frontier protection, and the loss of postal service routes under the United States government, as reasons for their separation.

Owings was elected again as provisional governor and Granville Henderson Oury was chosen as a delegate to petition for the territory's admission into the Confederacy.

Arizona was thought to be important to the role of the New Mexico Territory in the American Civil War primarily because it offered Confederate access to California.

With support from the secessionist residents of Mesilla, Baylor's 2nd Texas Mounted Rifles entered the territory and took a position in the town on July 25.

[5] On August 1, 1861, the victorious Baylor proclaimed the existence of a Confederate Arizona Territory, which comprised the area defined in the Tucson convention the previous year.

[6] The next month, Baylor's cavalrymen under Bethel Coopwood, marched north from Camp Robledo along the Rio Grande and surprised a Union force of New Mexican militia cavalry in a small engagement west of the Rio Grande at the village of Canada Alamosa, ending with another Confederate victory and the capture of 25 men of that unit including its commander.

Baylor sent Company A, Arizona Rangers to Tucson to protect the population from the Apache and delay the advance of Union troops from Fort Yuma.

The territorial government relocated to Franklin, then with Confederate military units retreated to San Antonio abandoning West Texas.

For the rest of the war, California Column troops controlled all of Confederate Arizona, Franklin and Fort Quitman in West Texas.

The government in exile remained in Texas for the duration of the war, although MacWillie continued to represent the territory in the First and 2nd Confederate States Congresses.