When the Muslim emperor Babur came down from Ferghana in 1527, he defeated the Hindu King of Chittodgad, Rana Sangrama Singh at Sikri, using cannon and artillery. After this victory, Babur took over the region, leaving his general, Mir Baqi, in charge as viceroy.

Mir Baqi allegedly destroyed the temple at Ayodhya, built by the Hindus to commemorate Rama's birthplace, and built the Babri Masjid, naming it after Emperor Babur. Although there is no reference to the new mosque in Babur's diary, the Baburnama, the pages of the relevant period are missing in the diary. The contemporary Tarikh-i-Babari records that Babur's troops "demolished many Hindu temples at Chanderi"

Palaeographic evidence of an older Hindu temple on the site emerged from an inscription on a thick stone slab recovered from the debris of the demolished structure in 1992. Over 260 other artifacts were recovered on the day of demolition, and many point to being part of the ancient temple. The inscription on the slab has 20 lines, 30 shlokas (verses), and is composed in Sanskrit written in the Nagari script. The ‘Nagari Lipi’ script was prevalent in the eleventh and twelfth century. The crucial part of the message as deciphered by a team comprising epigraphists, Sanskrit scholars, historians and archaeologists including Prof. A.M. Shastri, Dr. K.V. Ramesh, Dr. T.P. Verma, Prof. B.R. Grover, Dr. A.K. Sinha, Dr. Sudha Malaiya, Dr. D.P. Dubey and Dr. G.C. Tripathi.

The earliest mention of the Babri water well was in a two line reference to the Mosque in the Gazette of Faizabad District 1918 which says “There are no significant historical buildings here, except for various Buddhist shrines, the Babri Mosque is an ancient structure with a well which both the Hindus and Mussalmans claim has Miraculous properties.”

Ayodhya is a pilgrimage site for Hindus and the annual Ram festival is regularly attended by over 500,000 people of both the Hindu and Muslim faiths, and many devotees came to drink from the water well in the Babri Courtyard. It was believed drinking water from this well could cure a range of illnesses. Hindu pilgrims also believed that the Babri water well was the original well in the Ram Temple under the mosque. Ayodhya Muslims believed that the well was a gift from God. Local women regularly brought their new born babies to drink from the reputedly curative water.