Established in year 1510 by a Muslim Spiritual leader Zainudhin Makhdum, Ponnani Juma Masjid serves as the Mecca of Kerala Muslims. However, according to a record in Malabar Manual, historian William Logan said that this mosque was constructed in 925 Hijrah and once was the center of Islamic education for Kerala's Muslim community.
The mosque is said to be built by a Hindu artisan and a good friend of Makhdum Ashaari. The structure of this building depicts traditional architectural style of Kerala. Tomb of Ashaari, who later converted into a Muslim, is situated at the same place as of Makhdum.