During New Spain's insurgency

Banner with the image of the Virgin of Guadalupe carried by Miguel Hidalgo and his insurgent followers,
an act Abad y Queipo denounced as a sacrilege.

The Bourbon Reforms had resulted in the virtual exclusion of American-born Spanish men from attaining
high office, and increased alienation between peninsular-born Spaniards and the American-born. Abad y
Queipo recognized the criollos' resentment and suggested that the rift be softened by sending criollos to
Spain for education and that the crown appoint elite criollos to high positions in the government in
Spain, in the military and the Catholic Church, as well as allowing those in New Spain to be appointed to
high office in Peru and vice versa.[15] The increasing alienation of criollos from the Spanish crown flared
into open rebellion in 1810 with the revolt of secular priest Miguel Hidalgo.

Abad y Queipo had been friends with Hidalgo, who had come before the Inquisition. With the outbreak
of violence led by Hidalgo in September 1810, Abad y Queipo himself came under suspicion and was
denounced to the Inquisition by Fermín Peñalosa y Antón for his being "delinquent in matters of faith".
[16] Abad y Queipo strongly and energetically opposed the violent movement for Mexican
independence from Spain. This was perhaps due his belief that the economic and social progress he
sought was threatened with destruction by movement led by his friend Hidalgo.[17] Abad had also
sought the friendship of members of the revolutionary juntas of Valladolid (now Morelia) and San
Miguel el Grande (now San Miguel de Allende).

On 24 September 1810, Abad y Queipo published the decree excommunicating insurgents Hidalgo,
Ignacio Allende, Juan Aldama, and Mariano Abasolo. Hidalgo's excommunication was for Hidalgo's
having "raised a standard of rebellion and seduced a number of innocent people," but it was for
rebellion against the crown's authority not the Church's.[18] The insurgents disputed the legality of the
excommunication, based on the lack of papal approval of Abad y Queipo's appointment, which he
disputed, and Archbishop Lizana confirmed the order of excommunication.[19]

There were some prominent parish priests among the insurgents, most especially Hidalgo and José
María Morelos. Abad y Queipo claimed in September 1812 that the majority of priests were loyal to the
crown and few were insurgents, saying "even among Jesus's disciples there was a Judas."[20]
Contemporaries, including Lucas Alamán and later scholars have emphasized priests' participation in the
insurgency, and evidence shows that they participated in larger numbers than Abad y Queipo estimated,
but in fewer numbers than contemporaries thought.[21]

In 1815 Abad y Queipo sent another report to the king (Ferdinand VII now), denouncing the mistakes of
Viceroy Félix María Calleja and the lack of prudence of Lardizábal, minister of the Indies. Ferdinand
recalled Abad y Queipo to Spain since "he was suspected of dangerous liberal views."[22] He was
eventually confirmed as bishop of Michoacan, but could not return to Mexico. Following Mexican
independence in 1821, Abad y Queipo resigned that post and became bishop of Tortosa.[23]