However, experts have disputed claims that Serra was in any way involved in genocide, and in contrast, there is evidence that Serra advocated for the rights of the indigenous people in the face of mistreatment by the Spanish military.
A California archeologist, who has studied the missions for over 25 years, told CNA earlier this year that it is clear from Serra's own writings that he was motivated by a missionary zeal to bring salvation to the native people through the Catholic faith, rather than by genocidal, racist, or opportunistic motivations.
"Serra was a man on a mission," Dr. Ruben Mendoza, an archeologist and professor at California State University-Monterey Bay, told CNA.
"He was absolutely determined to engage the salvation of indigenous communities. And while for some that may be seen as an intrusion, for Serra in his time, that was seen as one of the most benevolent things one could do- to give one's life over to others, and that's what he did."
Born on the island of Petra Mallorca in Spain in 1713, Serra joined the Franciscans and quickly gained prominence as both a scholar and professor.
He chose to give up his academic career to become a missionary in the territory of New Spain, in which Spanish colonizers had already been active for over two centuries.
Traveling almost everywhere on foot and practicing various forms of self-mortification, Serra founded mission churches all along the coast- the first nine of the 21 missions in what is today California.
Many of the missions would form the cores of what are today the state's biggest cities- such as San Diego, San Francisco, and Los Angeles.
In many ways, the missions were a communal venture between the friars and Native leaders, Mendoza said. Soldiers were typically housed in a garrison just off-site from the compound. The compound itself would include work areas, such as a blacksmith's shop and places for crafts and weaving.
The Europeans taught the Natives new agricultural techniques, as well as instruction in the faith, performing thousands of baptisms.
Serra specifically advocated for the rights of Native peoples, at one point drafting a 33-point "bill of rights" for the Native Americans living in the mission settlements and walking all the way from California to Mexico City to present it to the viceroy.
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Mendoza said the worst abuses against the Native Americans in California took place after the age of the missions ended, when the Spanish government ceased sending funding to the 21 sites and to the Spanish military.
The soldiers, without the support of their faraway benefactors, began to prey on the missionaries and the Natives. Many more Natives died during this time than had in the 60 years that the missions were operational.
The California gold rush in the 1840s saw hundreds of thousands of European settlers come to the area, with little to no protections afforded to the Natives.
While many Native peoples did suffer horrific abuse, Mendoza said many people conflate the abuses the Natives suffered long after Serra's death with the period when Serra was alive and building the missions.
Pope Francis canonized Serra in 2015 during a visit to the United States.
"Junípero sought to defend the dignity of the native community, to protect it from those who had mistreated and abused it," the pope said in his homily at the Mass of canonization.