Kobo Daishi carved the temple's principal Amida Buddha statue in 807 and originally enshrined it in the Shinto shrine above. It wasn't moved to its current Buddhist temple home until over 1,000 years later.

Jinnein and Kannonji are the only two temples among all 88 Shikoku pilgrimage sites that share the exact same grounds, a unique arrangement created after Meiji-era religious reforms forcibly separated them from a Shinto shrine.