The Pilgrimage Centre at Carfin Grotto, North Lanarkshire opened in 1922 and attracts thousands of visitors each year.
But the Diocese of Motherwell said it was no longer "economically viable" to run the site, shop and café.
A petition to try and stop the closure received 5,000 signatures, however the decision to close the site is still going ahead.
Rt Rev Bishop Joseph Toal said: "The ultimate difficulty for the Centre is that not enough people visit the Grotto.
He said the centre has been "operating at a loss" for a number of years and is a business that "is not making money."
"We have been left with no option, but to make a difficult choice in regard to the Pilgrimage Centre.
"For the staff especially this is a sad moment and I thank them for their commitment and hard work over many years. I thank also those who have served as directors, especially at this difficult time."
"As a Diocese with more limited financial resources than in the past, we must cut our coat according to our cloth."
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