Aldama was in San Miguel when he heard news that the conspiracy had been betrayed by a supporter who informed the Spanish colonial authorities.

Aldama was captured by the Spanish colonial authorities on March 21, 1811 at the Wells of Baján in Coahuila.

He was court-martialed for insubordination towards the Spanish Crown and executed for treason, by firing squad on June 26, 1811, together with Allende and other members of the rebel army including Mariano Jiménez and Manuel Santa María.

Aldama's body was decapitated and his head taken to the Alhóndiga de Granaditas where it was shown to the public inside a cage hung from one corner of the building.

Finally, in 1925, his remains were moved one last time to the mausoleum in the Independence Column in Mexico City.