This infuriated the Apache chiefs Mangas Coloradas and (after the Bascom affair) Cochise, who by 1861 had formed an alliance with each other and vowed to destroy all of the Americans and Mexicans encroaching on their land.

The founder of Phoenix, Jack Swilling was a first lieutenant of the Arizona Guards, he is believed to have fought in the Pinos Altos engagement.

Most of the Arizona Guards were settlers and miners from around Pinos Altos and the Mimbres River valley or other parts of southern New Mexico Territory who had joined to protect their lives and property from the escalating conflict with the Mimbreños.

The combined force of Mangas Coloradas and Cochise numbered well over 300 strong when they turned their attention to Pinos Altos in the early morning of September 27, 1861.

Apache forces first attempted to burn several log cabins which ran along the perimeter of the settlement: this failed, and the natives were repulsed.

For a while the two sides fought at medium to long range until the Apaches launched a full attack around 12:00 noon, leading to hand-to-hand combat.

Within the last half-hour of the battle, Captain Thomas Mastin managed to turn an almost certain defeat into victory with his simple order to bring up the old cannon.

Captain Mastin was mortally wounded, sometime while leading the cavalry charge that decided the battle; he died a few days later at Pinos Altos.

Hardeman's troop came across the Apache trail and tracked them for days, all the way to the Gila River before turning back because their rations were running low.

On October 8, a distress message was sent from the miners of Pinos Altos, so 100 men were sent to reinforce the Arizona Guards, the largest Confederate force ever sent to relieve a town threatened by natives.