The Touws River Islamic Society bought the land in 2015 for the small Muslim community and passers-by who needed a place to pray.
Last year they applied for rezoning of the land, which was approved by the Laingsburg Municipality, provided certain conditions were met.
The church appealed the decision, and it was reviewed by the municipality’s town planner.
The church charged that a mosque right next to it “did not benefit the community”.
The church’s pastor Jerome Willemse said the mosque should rather be situated in the town.
Muslim Judicial Council (MJC) president Sheikh Irafaan Abrahams this week witnessed the signing of the go-ahead for the Laingsburg Mosque.
Ismail Bhyat, of the Islamic society, said at the time of the objection, in Ceres and Worcester there were churches and mosques opposite one another.
The mosque was essential for Muslim travellers from the N1, so much so that every town from Joburg to Cape Town has a place where Muslims could stop to pray.