People routinely throw coins into the famous tourist attraction in keeping with the legend that the act will bring good fortune and enable a return to the city.
From the start of April, the money will no longer be paid to Caritas to help the poor, but will be used by the city for restoration projects.
The proposal was reportedly approved by the council in December - drawing criticism from the Church.
Avvenire, the daily paper produced by the Italian Bishops' Conference, described the city's bureaucracy as "the enemy of the poor" in a front-page story headlined "money taken from the poorest".
This isn't the first time the Catholic charity has faced calls to stop collecting more than £1m from the Baroque fountain each year.
In 2017 Virginia Raggi, Rome's mayor, made the same proposal but it was delayed for a year following widespread criticism.
The charity asked the mayor on Twitter to reverse her decision and reminded her of the "5,000 volunteers, 300 social workers and 145 catholic centres" involved with the charity.
Caritas, which was founded in Rome in 1971, relies on the donations from the fountain to help the city's homeless and families struggling financially.
Premier has learned that the mayor of Rome is reconsidering the decision to divert the cash from the charity.
Catholic Journalist Andrea Gagliarducci who is based in Rome revealed to Premier: "I can give you breaking news - this morning the mayor of Rome Virginia Raggi, said that perhaps they should really discuss the decision that they made.
"So they're thinking about giving this money back to Caritas."