A colony has been roosting in St Hilda's Church at Ellerburn, close to the North York Moors.
But despite the church's best efforts the bats are not moving and are soiling the altar and church furniture, leaving the church with an "appalling smell".
The creatures are protected by law and cannot be wilfully disturbed.
Volunteers at the church have been working for the past decade to keep the altar, stonework and woodwork clean.
But the bats, roosting in the higher areas of the church continually soil the interior of the building with urine and faeces.
Church warden Liz Cowley said keeping the 11th Century building in good shape was difficult.
She said: "You can see the urine marks (on the altar), they won't go away.
"If people were coming in here damaging an ancient building like this, you would say it was criminal damage.
"The smell is appalling, it's a combination of ammonia from the urine and a musty smell from the droppings that catches at the back of the throat."
Members of the church had spent Â£10,000 trying to get the bats to move and had paid for specially-built lofts nearby.
The Rev Paul Mothersdale, the Rector of St Hilda's Church, said a lot of money had been invested in trying to persuade the bats to move out of the church.
The Rev Mothersdale said: "We've tried to do everything that English Nature, or Natural England, have wanted us to do.
"Money has been spent, not only by the congregation, not only out of church funds, but local people have mucked in and helped.
"And yet we're no further forward, we're still as we were 10 years ago."
Lucy Bellini, of Natural England, said the bats had to be carefully monitored.
Ms Bellini said: "It is a really regionally important roost.
"Because of that we need to be sure that there are replacement roosts that are suitable and that the bats have found and are aware of and can move to before we allow the church to seal up access points and move the bats out of the church."
A congregation in North Yorkshire has spent thousands of pounds building heated bat lofts in an attempt to lure the creatures out of their church.