With the population of Jantetelco, Matamoros created 2 regiments of cavalry, 2 battalions of infantry and 1 of artillery; in total his forces were composed by 2000 men.

During the Spanish siege of Cuautla, from February 9 to May 2 of 1812, Morelos recognized Matamoros' ability in the battlefield and promoted him to the rank of lieutenant general, effectively making him second in command of the army.

While serving as parish priest of Jantetelco, he was accused of sympathizing with the ideas of the Creoles in favor of independence, which is why he was reported to the Spanish authorities shortly before the war began.

He was able to escape to join the insurgent ranks of the priest José María Morelos y Pavón in Izúcar, on December 16, 1811.

Agustin de Iturbide attacked the Morelos army and it was a disaster; in the middle of the confusion, Matamoros tried to escape crossing the river (close to Puruaran) but was captured by Eusebio Rodríguez, a soldier from the battalion of "Frontera", who received 200 pesos and a promotion.