All Saints Church in Braunston-in-Rutland was one of the first churches to receive money from a £3.8m Heritage Lottery Fund to reduce the impact of bats on the buildings across the country.
The scheme has allowed the church to fill gaps in the ceiling to prevent poo and urine getting through, without harming the animals.
Sue Willetts, church warden at All Saints Church, said: "Before, we had covers down on the floors to collect the droppings.
"We had to clean the pews every time, it took an hour before every single service. Now we use the church how it's meant to be."
The church has 500 bats living in its roof. They cannot be removed because they are a protected species.
Rosemary Riddell, from the Bat in Churches project, said work at All Saints Church "has enabled us to sort of roll out solutions to other churches similar to Braunstone and it's really helped us to learn from their experiences".
"[The church] was one of our guinea pigs and we're grateful for their engagement and involvement," she said.
In 2014, local MP Sir Alan Duncan said the bat droppings problem at the church as "absolutely intolerable."
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