The theft happened shortly after 2:45 p.m. on Saturday after Father Gerardo Menchaca just finished a baptism ceremony.
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"As a priest, I would never expect someone to come here with intention of stealing," said Fr. Gerardo Menchaca. "You're robbing not only money, but you're robbing gifts for children."
Surveillance video obtained by ABC7 News shows two masked intruders wearing sunglasses and gloves enter the church through a side entrance and then carrying out a large, wooden donation box by the pulpit.
Later, a church official noticed another smaller donation box had the lock broken and the money inside of it was was also stolen.
Father Menchaca estimated anywhere from $2,000 to $3,000 was stolen from the church.
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He said the money goes to an annual toy drive for children of the congregation and are handed out at a celebration of the Three Kings on Jan. 6 of each year.
Now father Menchaca is hoping the thieves have a change of heart and return the money.
"It's upsetting, but at the same time I am inviting the community to pray for these individuals. I hope and pray that they will listen to this message and that they will repent," said Fr. Menchaca.
He is also asking for members of the community to give what they can so the annual tradition is not ruined for the church's children.
Members of the community are answering the priest's call.
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San Jose resident Ben Watkins, who attends another church, stopped by Christmas Eve looking to donate after hearing about what happened.
"I'm sure they will be able to make up the money and then maybe even get some extra," said Watkins, "Maybe it turns out to be a positive in the long run."
At around Tuesday at 6p.m., we found out the church has passed its $5,000 fundraising goal in less than three hours.
If you would like to help, here is a link to their GoFundMe.