The Ponnani Juma Masjid was built about 600 years ago by Zainuddin Ibn Bin Ahmed (Zainuddin Makhdoom I).  Zainuddin Makhdoom II, it is believed, used to sit in the mosque while he worked on his famous book Tuhfatul Mujahideen, a historical account of Malabar.

A lamp, believed to be more than 500 years old and used by Zainuddin Makhdum II, stands in the middle of the prayer hall of the mosque. It is said that the students who came here, from Sumatra, Java and Ceylon, to learn the tenets of Islam used to sit beside the lamp. The mosque played an important part in imparting Islamic doctrines and philosophy and gave birth to many religious leaders.

There is a sword in the Juma Masjid believed to have been displayed during sermons at the mosque, around 200 years ago. Koranic inscriptions can also be seen on the entrances of the mosque. 

For the construction of this mosque built in the Kerala style of architecture, wood has been used extensively. It is said that the mosque was built by a Hindu carpenter who later converted to Islam. He had been a close friend of Zainuddin. The tombs of Makhdoom I and the carpenter, who came to be known as Asari Thangal, can be seen at the mosque.

The major festival (nercha) of the mosque falls in the month of March/April and lasts four days.

Near the mosque is the mausoleum of the Malappuram martyrs. These martyrs’ brave deeds are described in the Moplah ballads.