Jaunpur was then a major center of Urdu and Sufi knowledge and culture. The Sharqi dynasty was known for its excellent communal relations between Muslims and Hindus, perhaps stemming from the fact that the Sharqis themselves were originally indigenous converts to Islam, as opposed to descendants of Persians or Afghans. Jaunpur’s independence came to an end in 1480, when the city was conquered by Sikander Lodhi, the Sultan of Delhi. The Sharqi kings attempted for several years to retake the city, but ultimately failed.

Although many of the Sharqi monuments were destroyed when the Lodhis took the city, several important mosques remain, most notably the Atala Masjid, Jama Masjid (now known as the Bari (big mosque) Masjid) and the Lal Darwaza Masjid. The Jaunpur mosques display a unique architectural style, combining traditional Hindu and Muslim motifs with purely original elements. The old bridge over the Gomti River in Jaunpur dates from 1564, the era of the Mughal emperor Akbar. The Jaunpur Quilla, a fortress from the Tughlaq era, also remains in ruined form.

Jaunpur district was annexed into British India based on the Permanent settlement of 1779, and thus was subject to the Zamindari system of land revenue collection. During the Revolt of 1857 the Sikh troops in Jaunpur joined the Indian rebels. The district was eventually reconquered for the British by Gurkha troops from Nepal. Jaunpur then became a district administrative center.

Modern Jaunpur district shares the underdevelopment of most of Eastern Uttar Pradesh. There are currently no major industries operating in the city, and traditional industries such as perfume making have become increasingly unviable. Under the initiative of the UP government, an Industrial Area has been set up in the Sathariya region of the district to promote industrial growth and expansion. Land is being allotted to budding industrialists and the government has plans to help people of this region develop more and more industries. During the past three years Jaunpur city has experienced a growing corporate presence in financial services as well as in the organized retail sector.

Politically, Jaunpur is divided between the Samajwadi Party (SP) which tends to represent the interests of the Backward Castes and the Bahujan Samaj Party (BSP) which tends to represent the interests of the Scheduled Castes, though other political parties too have a significant presence.

Jaunpur is the district headquarters. The district has 3 Lok Sabha and 10 Vidhan Sabha constituencies.