San Ignacio is the capital of the Moxos Province and is situated at an elevation of 144 m above sea level at Laguna Isiboro, a lake of 20 km2 west of the town.

San Ignacio is located 100 km south-west of Trinidad, the department's capital.

San Ignacio de Moxos is located in the wettest region of the Beni department, situated on the border between the Amazon rainforests of the Chapare region, and the monsoonal llanos of western Santa Cruz and southwestern Beni.

While San Ignacio de Moxos experiences a short dry season, rain is plentiful year round, and temperatures are generally warm to hot.

Camba Spanish is the primary vernacular lingua franca spoken in the town.