Naason Joaquin Garcia and a follower of La Luz del Mundo, 24-year-old Susana Medina Oaxaca, were arrested after landing at Los Angeles International Airport, California attorney general Xavier Becerra's office said.
Around 1,000 worshippers gathered at the headquarters of La Luz del Mundo in Guadalajara, Jalisco, Mexico, to pray for Garcia as he was held in Los Angeles on 25 dollars million (£20 million) bail.
The 50-year-old, known as "the Apostle" among his followers faces 26 counts ranging from human trafficking and production of child pornography to rape of a minor. The charges detail allegations involving three girls and one woman between 2015 and 2018 in Los Angeles County.
The church, whose name translates as the Light of the World, was founded in 1926 by Garcia's grandfather. It has been the subject of child sex abuse allegations for years but authorities in Mexico have never filed criminal charges.
It has more than 15,000 churches in 58 countries, according to its website.
Garcia - who was a minister in Los Angeles and other parts of southern California before becoming the church's leader - coerced the victims into performing sex acts by telling them that refusing would be going against God, authorities said.
"Crimes like those alleged in this complaint have no place in our society. Period," Mr Becerra said in a press release. "We must not turn a blind eye to sexual violence and trafficking in our state."
The investigation began in 2018, prompted in part by a tip to the state's Department of Justice through an online clergy abuse complaint form.
David Correa, a spokesman from the church's headquarters, said they learned about the charges from the media.
"We categorically deny those false accusations," he said. "We know him personally and he is an honourable and honest man."
Church officials said Garcia has always behaved lawfully and they rejected the attorney general's charges.
A third follower, Alondra Ocampo, 36, was arrested in Los Angeles County and held ahead of arraignment in Los Angeles. A fourth defendant, Azalea Rangel Melendez, is at large.
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