The Turkish conquest of the subcontinent was a long, drawn-out process covering several centuries. It began in Afghanistan with the military forays of Mahmud of Ghazni in 1001. By the early thirteenth century, Bengal fell to Turkish armies. The last major Hindu Sena ruler was expelled from his capital at Nadia in western Bengal in 1202, although lesser Sena rulers held sway for a short while after in eastern Bengal.

Bengal was loosely associated with the Delhi Sultanate, established in 1206, and paid a tribute in war elephants in order to maintain autonomy. In 1341 Bengal became independent from Delhi, and Dhaka was established as the seat of the governors of independent Bengal.

Turks ruled Bengal for several decades before the conquest of Dhaka by forces of the Mughal emperor Akbar the Great (1556-1605) in 1576. Bengal remained a Mughal province until the beginning of the decline of the Mughal Empire in the eighteenth century.

Under the Mughals, the political integration of Bengal with the rest of the subcontinent began, but Bengal was never truly subjugated. It was always too remote from the center of government in Delhi. Because lines of communications were poor, local governors found it easy to ignore imperial directives and maintain their independence. Although Bengal remained provincial, it was not isolated intellectually, and Bengali religious leaders from the fifteenth century onward have been influential throughout the subcontinent.

The Mughals in their heyday had a profound and lasting effect on Bengal. When Akbar ascended the throne at Delhi, a road connecting Bengal with Delhi was under construction and a postal service was being planned as a step toward drawing Bengal into the operations of the empire. Akbar implemented the present-day Bengali calendar, and his son, Jahangir (1605-27), introduced civil and military officials from outside Bengal who received rights to collect taxes on land. The development of the zamindar (tax collector and later landlord) class and its later interaction with the British would have immense economic and social implications for twentieth-century Bengal. Bengal was treated as the "breadbasket of India" and, as the richest province in the empire, was drained of its resources to maintain the Mughal army. The Mughals, however, did not expend much energy protecting the countryside or the capital from Arakanese or Portuguese pirates; in one year as many as 40,000 Bengalis were seized by pirates to be sold as slaves, and still the central government did not intervene. Local resistance to imperial control forced the emperor to appoint powerful generals as provincial governors. Yet, despite the insecurity of the Mughal regime, Bengal prospered. Agriculture expanded, trade was encouraged, and Dhaka became one of the centers of the textile trade in South Asia.

In 1704 the provincial capital of Bengal was moved from Dhaka to Murshidabad. Although they continued to pay tribute to the Mughal court, the governors became practically independent rulers after the death in 1707 of Aurangzeb, the last great Mughal emperor. The governors were strong enough to fend off marauding Hindu Marathas from the Bombay area during the eighteenth century. When the Mughal governor Alivardi died in 1756, he left the rule of Bengal to his grandson Siraj ud Daulah, who would lose Bengal to the British the following year.