The town is located along the upper part of the River Ter, in the valley of the same name, and enclosed by the Serra Cavallera to the north and the mountain of Sant Antoni to the south. It has an inland, continental climate, with abundant precipitation and notable temperature variability.

Most of the economy of Sant Joan de les Abadesses is centered on industry and manufacturing. However, there have more recently been increases in tourism to the town, with a corresponding increase in the service industry. Rural areas of the municipality are largely occupied by farms, usually raising cows.