If they resisted or said they would leave, leaders threatened to take away their children, deny them transportation home and told them that their loved ones had rejected them and that “only God” loved them, according to prosecutors. Others were forced to hand over personal property, passports and immigration papers to ensure they would not leave, prosecutors said.

The money was partly used to pay for the expansion of Imperial Valley Ministries, the authorities said. Founded in the 1970s, its stated mission is to “restore” people with drug-related problems at faith-based rehabilitation homes, according to prosecutors. The organization ran about 30 affiliate churches throughout the United States and Mexico, prosecutors said.

After the May 2018 raids — when federal agents confiscated computers, cellphones and more than $45,000 in cash from several properties — Mr. Gonzalez told local reporters the money was used “to pay for the cars, to pay for the bills.”

But former members and those familiar with the church’s activities have described exploitative practices and dismal outcomes.

Shaunte Martinez, a former resident and a homeless woman from El Centro, told a reporter she was shocked by the restrictions and expectations in the homes and described it as “brainwashing.”

“They wanted me to speak in tongues and I wouldn’t,” she said.

Ms. Martinez said that she later became homeless again.

Jessica Solorio, founder of Spread The Love Charity, told a local news station KYMA in 2018 that her organization had helped people leaving Imperial Valley Ministries.

“The ones that came into our center told us that they were brought under false pretenses, they weren’t exactly sure what they were getting into,” she said. “So, one way or another, they would leave the program, and were stuck in El Centro homeless.”