The Church of Scientology has always been a bone of contention between the couple and Tom wanted three-year-old Suri to be raised a Scientologist.
But last week Katie enrolled the toddler at the Catholic Charities Yawkey Centre For Early Education And Learning in Boston, Massachusetts.
The family are living in the city while Tom, 47, films his new movie, the spy comedy thriller Wichita. Katie's mother also flew in for her granddaughter's first week at the pre-school.
'Katie has been listening to her parents who are devout Catholics,' I'm told.
'She is not convinced by Scientology and has told Tom that she wants Suri to be educated as a Catholic - as she was.
'They had been having huge problems agreeing on her school. To say they were having arguments is putting it mildly - but Tom came around to the idea in the end.'
Holmes, 30, has not been seen at the Church of Scientology for more than five months.
But Cruise, who was also raised Catholic but converted to Scientology in 1990, remains an ardent follower.
