He grew up in the Cumberland Mountains in eastern Tennessee, and his grandfather had established a settlement known as Bean's Station.

He continued on to Natchez, Mississippi, where he joined Philip Nolan's last filibustering expedition to Spanish Texas, on the promise of riches from captured mustangs and perhaps gold and silver.

On May 21, 1801, a Spanish force of 120 men under the command of Lieutenant Miguel Francisco Múzquiz left Nacogdoches in pursuit of Nolan, whom they encountered entrenched and unwilling to surrender just upstream from where the current Nolan River flows into the larger Brazos (now in Hill County, Texas).

He remained in prison there until November 1811, when he was released after volunteering to fight for the Spanish Royalists against the insurgents under General José María Morelos, who was besieging Acapulco.

Bean rose in rank and favor in the insurgent army, in large part because of his knowledge of munitions.

Fifteen years after leaving the United States, Bean returned as a Mexican colonel and emissary from Morelos to seek American aid for the insurgents, but without much success.

On February 18, 1815, Bean sailed on the Águila to return to Mexico, but he soon was sent back to New Orleans as the escort of the Mexican emissary to the United States, José Manuel Herrera, and Morelos's son, Juan Almonte.

Bean married Magdalena Falfán de los Godos, a lady of "fine family", intending to return with her to the United States.

He stayed in the Neutral Ground (between the Louisiana Purchase, belonging to the United States, and Spanish colonial New Spain), working on his memoirs.

With news of Mexican independence, in 1823 Bean moved with his family to Nacogdoches, Texas, intending to seek reward for his revolutionary services.

In 1825 Bean went to Mexico City, where he received a land grant and was commissioned as a colonel in the Mexican army.

He applied for colonization rights to the border reserve along the Sabine River, but Mexico awarded them to Lorenzo de Zavala instead, in 1829.

After Texas gained independence, Bean continued to live around Nacogdoches until 1843, when he returned to Jalapa, Veracruz and his first wife.