José Manuel Gallegos was born in Abiquiú, New Mexico, on October 30, 1815, to Pedro Ignacio, the alcalde (mayor) and chief magistrate of the town, and Ana María Gavaldon. He attended a parochial school in Taos, New Mexico, where he became interested in theology, and may also have attended a private school in Abiquiú. From 1836 to 1839, he studied at the College of Durango, Mexico, to prepare for the Catholic priesthood. Gallegos most likely graduated and was ordained by 1840. His mentors, including Padre Antonio José Martínez, studied in Durango during the Mexican Revolution, immersing themselves in secular politics as much as in sacred texts. Having committed to Mexican nationalism in their youth, they imparted that cultural identity to a young generation of seminarians like Gallegos, imbuing them with a deep sense of loyalty to the nascent Mexican state.

Gallegos served in San Juan from 1840 to 1845 and in the parish of San Felipe Neri, Albuquerque from October 1845 to September 1852, becoming pastor of the latter parish in December 1847. In July 1850, almost two years after the United States acquired New Mexico in the Treaty of Guadalupe Hidalgo, the Catholic Church placed the territory under the ecclesiastical control of the U.S. Catholic hierarchy. Pope Pius IX chose a young French missionary, Jean Baptiste Lamy, to manage the effort. Lamy was consecrated as a bishop in November 1850 and named Joseph Projectus Machebeuf as his Vicar General. Bishop Lamy and Machebeuf arrived in Santa Fe in August 1851, but the Vatican failed to inform the incumbent bishop, Antonio Zubiría y Escalante, about the administrative change.

During the ecclesiastical and political confusion Gallegos served on the Legislative Assembly of the Department of Nuevo México from 1843 to 1846. When the Treaty of Guadalupe Hidalgo ended the Mexican-American War (1847-1848), New Mexico became a territory of the United States. Gallegos was elected to the first Territorial council of New Mexico in 1851.
During the transfer of power from Bishop Zubiría to Bishop Lamy, a power struggle ensued because Gallegos and the native clergy were reluctant to accept the new authority and continued their allegiance to the Bishop of Durango. Because of his record, Gallegos proved an easy mark for Lamy, who questioned his competence, loyalty, and integrity and eventually suspended him from the priesthood in 1853. Two reasons are cited for Gallegos’s punishment. First, Gallegos left his parish to travel to Mexico without official permission and, upon his return, tried to rally support among his parishioners against Machebeuf, whom Lamy had handpicked to succeed him. Second, based principally on rumor and innuendo, Gallegos was charged with violating his vow of celibacy. Gallegos would latter make the statement that he was, “deprived of [his] living … by the new French bishop, to make way for the imported French priests of his own selection.”

Beginning in the summer of 1853, Gallegos dedicated himself completely to his political career. In part due to the support and guidance of David Merriwether, a Democrat who would later become Governor of New Mexico, Gallegos changed his allegiance to the United States. Merriwether instructed Gallegos on the principles of the Democratic Party. Gallegos did not speak English fluently, so he had Merriwether write down everything, and later had it translated into Spanish. Gallegos also had the support of the Penitentes, a New Mexican lay religious brotherhood. Gallegos was able to win the Democratic nomination for U.S. Delegate, despite the opposition from New Mexican politicians who called themselves the "American Party" and nominated James Carr Lane.

Gallegos won the election, and in March 1853, he left for Washington to begin his service as Delegate to Congress. The election was contested by James Carr Lane. Even though the House Committee on Elections found no grounds for supporting the charge, this action nonetheless set a precedent of contesting New Mexican elections, which lasted well into the twentieth century. During Gallegos' first term as Delegate, Congress did not take much interest in the territories except for the Indian question, which involved the property rights of citizens of states versus the rights of the Native Americans. Congress did, however, pass a number of appropriations which included funds for the territory of New Mexico such as public buildings, territorial government expenses, and the authorization for the employment of a translator.
Gallegos won the election to a second term, but he was denied his seat because of a powerful speech that his political opponent Miguel A. Otero delivered on the floor of the House contesting Gallegos' election. Otero appealed to the House on the basis of his loyalty to the United States despite his being a "native citizen" of what recently had been a part of Mexico. He said he was the first to come to the Congress of his "adopted fatherland" who could address the House "in the language of its laws and its constitution." The House seated Otero even though Gallegos, the incumbent, had a purported slim majority of the votes in the election, which Otero claimed were from Mexican citizens who had voted illegally.

Otero’s allies rehashed the smear tactics of earlier campaigns, advertising Gallegos’s dismissal from the Catholic Church. Bishop Lamy endorsed Otero and commanded clergy to support him. The initial count of the election results had Gallegos prevailing, with a razor-thin margin of 99 votes out of almost 14,000 cast.

Gallegos used the bulk of his speech to rebut Otero’s case point by point. He denied allegations that the Roman Catholic Church helped secure his election. Just the opposite was true, he argued. “This foreign bishop [Lamy] did … intermeddle, by himself and his priests, not to support, but to crush me, and to secure the election of my opponent.” Gallegos also challenged the results of the election report that threw out more than 130 “Mexican votes” for him, dismissed testimony from key elected officials, and presented signed testimonies on his behalf from disputed polling places. He reiterated the provisions of the Treaty of Guadalupe Hidalgo, which extended citizenship to Mexicans after one year, and submitted additional testimony from the secretary of the territory that contradicted some of Otero’s key claims. By his count, he had prevailed with close to 600 votes.

Granted permission to speak on the floor, Otero rejected the argument that cultural familiarity with the populace trumped the English proficiency required to represent them on the floor of the House. “I protest against the assumption the personal deficiencies or errors of the gentleman are to be imputed by representation to the people of our territory,” he said. Gallegos, he noted, broke his campaign promise that he would master English and would be “capable of representing the people here by his acquaintance with your language.” Otero also defended Bishop Lamy, insisting that he was not “guilty of any interference whatever unless that could be called an interference which sought … to restrain the priesthood from the scandal of an active and zealous participation in the canvass” on Gallegos’s behalf. In the end, his forceful presentation, with carefully crafted allusions to his loyalty to the “American party” and Anglo political institutions, won the day. Even Pennsylvania’s John Cadwalader, who studied the case and claimed to have “as strong an impression in favor of the sitting Delegate, as any member on this floor,” was persuaded by Otero’s case. The House overwhelmingly accepted the Election Committee’s recommendation, granting Otero a seat by a 128 to 22 vote.

Despite this setback, Gallegos returned to New Mexico and continued with his political career. In 1860 he was elected to the Territorial House of Representatives as the representative from Santa Fe; he served as Speaker of the House from 1860 to 1862. In 1862 he was defeated in his reelection bid. That same year the Texas Confederate troops took him prisoner. At the outbreak of the Civil War, Gallegos became a fervent Union supporter and provided information and assistance to Union forces when Confederates took over Santa Fe.

Gallegos served as treasurer of the territory from 1865 to 1866 and superintendent of Indian affairs for New Mexico in 1868. He returned to the U.S. House of Representatives as a Delegate from New Mexico in the 42nd Congress, but was unsuccessful in his bid for reelection in 1872. After 1873, Gallegos retired in New Mexico. At the age of 60, Gallegos died of a stroke on April 21, 1875, in the city of Santa Fe. Padre Gallegos was one of the most colorful pastors in the books of San Felipe. He along with other native clergy in New Mexico, were a point of contention to Bishop Lamy leading to a great rift that would root itself in the turbulent ecclesial-political history in New Mexico.