On the 29th, Union scouts approached Newtonia but were chased away. Other Federal troops appeared in nearby Granby where there were lead mines, and Cooper sent some reinforcements there. The next morning, Union columns appeared before Newtonia and fighting ensued by 7:00 am. The Federals began driving the enemy, but Confederate reinforcements arrived, swelling the numbers. The Northerners gave way and retreated in haste. As they did so, additional Union reinforcements appeared and helped to stem their retreat. They soon renewed the attack, threatening the Confederate's right flank. But newly arrived Confederates stopped the assault and eventually forced the Federals to finally retire.
Pursuit of the Federals continued after dark. Union gunners posted artillery in the roadway to halt the pursuit. As Confederate gunners observed the enemy artillery fire for its location, they fired back, creating panic. The Union retreat turned into a rout as some ran all the way to Sarcoxie, more than ten miles away. Although the Confederates won the battle, they were unable to maintain themselves in the area given the great number of Union troops. Most Confederates retreated into northwest Arkansas. The 1862 Confederate victories in southwestern Missouri at Newtonia and Clark’s Mill were the South’s apogee in the area; afterwards, the only Confederates in the area belonged to raiding columns.
Newtonia was one of the few battles during the Civil War in which Native Americans played a significant role on both sides.