It happened inside the Church of St. John the Baptist in Midtown.
The burglary was captured on surveillance video.
The poor boxes were ripped apart and their cash donations stolen by burglars.
"I'm very sad because the money served is hard earned money and we try to give it to the church," said Helen Hinbint, a church member.
Surveillance video captured the images of what appeared to be two thieves, who went after all of the donation boxes around the church.
They also got into the church supply room to commit the crime after climbing over a fence and breaking in through a window.
"The only way to describe it, probably, the feeling is that it was a real sense of being violated," said Fr. Thomas Franks, of St. John the Baptist Church.
The timing of the thefts was no accident.
"People are always particularly kind and generous at Christmas time, so we estimate that there were probably a few thousand dollars lost from the poor boxes themselves," Fr. Franks said.
A computer was also taken from the church office. Church leadership is thankful that they left behind ceremonial chalices, which are even more valuable than the stolen cash.
"Each chalice could be, some of the old ones, could be worth in excess of $10,000 or $15,000 for one chalice," Fr. Franks said.
But the stolen cash threatens the church mission of donating food to the poor through its food pantry.
"It's not really for me to judge what somebody does, but the actions seem wrong to me," said Ian Conroy, a church member.