The thieves struck at St Oswald's in the village of Methley on Monday evening, taking part of a path as well as coping stones from a wall.
In an online appeal, the church said: "Sadly we were targeted by thieves who stole part of our stone path and some of the coping stones from the churchyard wall.
"They seem to have also dumped all their rubble in amongst some graves and memorials. Please take care on the path until we can sort out repairs."
The church went on to share an image of the markings which had been made on all its Yorkshire stone paving.
Anyone who has been offered Yorkshire stone marked with crosses was urged to call the church or police via 101.