But Serra's defenders say that Serra was actually an advocate for native people and a champion of human rights. They note the many native people he helped during his life, and their outpouring of grief at his death.
Biographers note that Serra frequently intervened for native people when they faced persecution from Spanish authorities. In one case, the priest intervened to spare the lives of several California natives who had attacked a Spanish outpost.
In one letter urging fair treatment of native people, Serra wrote that "if the Indians were to kill me...they should be forgiven."
Los Angeles Archbishop Jose Gomez said in 2015 that Serra had "deep love for the native peoples he had come to evangelize."
"In his appeals, he said some truly remarkable things about human dignity, human rights and the mercy of God," the archbishop added.
In 2017, Gomez praised Serra as an overlooked American founder.
"Remembering St. Junípero and the first missionaries changes how we remember our national story. It reminds us that America's first beginnings were not political. America's first beginnings were spiritual," Gomez said in a 2017 homily.
Pope Francis canonized the Franciscan missionary in Washington, D.C. on Sept. 23, 2015.
"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. "Mistreatment and wrongs which today still trouble us, especially because of the hurt which they cause in the lives of many people."
The legacy of the Church, Cordileone said, is "a wonderful legacy that we should be proud of. There are those who want us to be ashamed of it. We have every reason to be proud of it."
"But also we have to approach living our Christian life with humility and to continue to give goodness to the world, and to give the world beauty and truth, with the help of the grace of God," he said.
"Our Lady is always asking us to pray the rosary,'" he added. "The rosary has the power even to change history"
Cordileone said Serra had a personal importance for him.
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"He was someone who was very much a part of my life growing up," said the archbishop.
"I grew up very close to the first mission he founded, in San Diego."
The toppling of the statue made him "very distressed" and "inflicted a great wound in my soul."
"So the presence of so many people here was of great support to me," he said.
In a June 20 statement, Cordileone said that important protests over racial injustice have been "hijacked" by a mob bent on violence.
"St. Serra made heroic sacrifices to protect the indigenous people of California from their Spanish conquerors, especially the soldiers," he said. "Even with his infirm leg which caused him such pain, he walked all the way to Mexico City to obtain special faculties of governance from the Viceroy of Spain in order to discipline the military who were abusing the Indians. And then he walked back to California."