He now leads a department that is still reeling from a jail abuse scandal that took down former Sheriff Lee Baca and several of his top aides, and is facing questions over racial profiling and deputy tattoos.
"There will be a learning curve. But this is a man with a Ph.D. He is no dummy," said Capt. Eli Vera about Villanueva, who earned the degree in public administration at the University of La Verne. The two worked together when they were sergeants at the Lennox station in the early 2000s, and Vera consulted on Villanueva's campaign.
Indeed, Villanueva has been quietly developing his political career for decades.
At 29, he ran for City Council in San Dimas, losing by just 44 votes. The next year, the young deputy announced his candidacy against former Sheriff Sherman Block in the 1994 election, saying, as he does today, that he would improve deputy morale. He eventually abandoned the campaign but kept mulling another run.
It was around this time that an undergrad at California State University, Los Angeles named Vivian Lopez was embedded with a Sheriff's Department narcotics team during an internship. An undercover surveillance mission she attended was nearly botched when a deputy in thick bifocals showed up unannounced in a marked patrol car.
"He's gonna ruin it for us!" she recalled thinking. "Well, three years later, I marry the guy."
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Vivian Villanueva served many years as a deputy, while helping to raise her husband's son from a previous relationship.
"He has always been the underdog," she said, adding that her husband deeply wants to help people and call out injustice.
His intense fixation and frankness have sometimes been off-putting in a department where social relationships are key, according to some who have worked with him.
"I even had people who would not want to be near me because they thought Alex was a black cloud," Vivian said.