The perpetrators raided the candle boxes in St Michael’s Church on Denmark Street.
They targeted the boxes where people light a candle in memory of, or for loved ones, at 5.30pm on Saturday, August 3.
It’s understood they picked the lock.
The same suspects then returned the following day and cleaned out the money box again.
“Somebody goes to a shrine, puts in money to pray for someone who is sick, or someone who has died and somebody comes along then and steals that money…” said Fr McDonnell, who contacted gardai.
“The guards have the video footage. The reason I reported is because if they're coming into us, they could be going into other churches as well,” said Fr McDonnell
Gardai confirmed to Limerick Live that sums of cash were taken in the course of the incidents.
“Investigations are ongoing at this time,” said the garda spokesperson.
The Limerick diocese has actually lost out three times - the two thefts and having to carry out repairs.
“As I said to the guards, it's one thing taking money out of the shrines but then you have to go and get a locksmith in and a welder to make another box. It is Church income,” said Fr McDonnell.
New security measures have been put in place in St Michael’s to try and prevent future thefts.
St Michael’s Church made headlines for a happier reason last year.
A golden statue of Michael the archangel, spear in hand standing upon a snarling dragon, which sits atop the church’s bell tower was completely restored.
The statue was first unveiled on September 29, 1881, the Feast Day of St Michael.
Two of those involved in the restoration project - Dr Paul O’Brien and Fionan Coughlan made a startling discovery that on this day each year the rising sun lines up with the spear held in the angel’s hands.
“It's just beautiful. It lights up every night. You wouldn't see it anywhere else. If somebody asked from a spiritual point of view, what's unique about Limerick then it’s that statue.
“We put out a public appeal to raise money for the works and within a year it was totally paid off,” said Fr McDonnell.