Pope Francis also allegedly told him that his sexuality "does not matter", Cruz told CNN.
"It goes beyond 'who am I to judge?' to 'you are loved by God, '" Christopher Lamb, the Vatican correspondent for the Catholic newspaper Tablet, told The Guardian.
"God loves all his children, however they are; you are a son of God, who accepts you exactly as you are". During their meetings, Cruz said the Pope addressed homosexuality, which has been traditionally deemed as a sinful practice in the Catholic church.
A year later, Pope Francis released the 256-page document "The Joy of Love", which encouraged individual conscience to be the guiding principle for Catholics negotiating the complexities of sex, marriage and family life.
Cruz said that the pope told him: "You know Juan Carlos, that does not matter". It marked the first time a reigning pope had visited the Holy Land, but at the time the Vatican did not recognize Israel as a state, and Paul did not pronounce the word "Israel".
For the gay community, the reported comments by the Pope are a great sign of hope for an evolved Catholic religion that is accepting of everyone, regardless of sexual orientation.
Cruz is one of three victims of Father Fernando Karadima who were in Rome in late April for three days of meetings with Francis.
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While some have hailed Francis' alleged comments as an open acceptance of homosexuality by the head of the Catholic church, it is possible, if Cruz's claim is true, Francis meant to distinguish between God's love for Cruz as a person and God's stance toward Cruz's homosexual acts.
The Pope is not changing official Church teaching, but he is at least signalling a much more open and inclusive approach, which will upset many conservative Catholics.
"They had told him that I didn't believe, that I was an enemy of the Church", Cruz said, according to Crux.
During that flight, he spoke about receiving Neria in the Vatican- without actually giving names, saying that "Life is life, things have to be accepted as they come".
DeBernardo noted other supportive remarks the pope had made privately to LGBT people, such as a transgender man in Spain and a gay man he met with during his 2015 US visit who had been a student of his in Argentina.
Growing up gay in the Catholic church is challenging.
As Pope Francis told a group of Salvadoran pilgrims in 2015, even after his death Blessed Romero "was defamed, slandered, his memory tarnished, and his martyrdom continued, including by his brothers in the priesthood and in the episcopate".