After the fall of the Karrani power in 1576, Bengal was under the mughal rule. But the establishment of effective rule took some time. On 19th December, 1578, Khan-i-jahan died and Muzaffar Khan became the governor of Bengal. Akbar's brother Mirza Hakim declared himself independent in Kabul, and Muzaffar Khan was defeated by rebels sympathetic to him, and Bengal and Bihar was declared to be his. He sent a subedar (governor) to Bengal, but lots of Afghans took control of parts of Bengal and all of Orissa. In April 1582, Akbar sent Khan-i-Azam as the subedar of Bengal, who won partial victory; but parts of the region remained under Masum Kabuli and Isha Khan, even under the next subedar Shahbaz Khan. In June 1584, Kutlu Khan of Orissa, who had revolted and took over parts of Bengal, was defeated. In 1586, both Isha Khan and Masum Kabuli accepted mughal overlordship. A new administrative system headed by a sipahsalar (later called subedar) started: Wazib Khan was the first sipahsalar, but he died in August 1587. He was followed by Sayyid Khan (1587–1594).
Raja Mansingh (1594–1605) was the next governor of Bengal. He shifted the capital from Tanda to a new town of Akbarnagar. There were again revolts headed by Isha Khan and Raghudeva, cousin of Lakshminarayana, ruler of Coochbehar. Mughals suffered heavy losses, but the revolt was suppressed. In 1598, Mansingh took temporary retirement, and his eldest son Jagatsingh took over. When he died, the younger Mahasingh took over. Because of revolts, Mansingh had to return to Bengal and defeat them in February, 1601; though revolts continued till next year. He also defeated the Mags of Arakan. The mughal empire passed on to nur-ud-din Muhammad jahângîr (1605–1627) who replaced Mansingh by Qutb-ud-din Khan Koka (1605–1607). He and Sher Afghan Istalaju, a Turk Jaigirdar in Bengal, quarreled and both died in 1607. Sher Afghan's wife finally married Jehangir and was called Nur Jahan.
The next subedar was Quli Khan (1607–1608) and when he died, Islam Khan (June 1608–died August 1613). Even at this time large parts of Bengal, under the zamindars known as bAro bhuJA. Examples of zamindars who often revolted are Musa Khan, son of Isha Khan (controlled Dhaka, half of Tripura, Maimansingh, Rangpur, and parts of Bagura and Pabna), Bahadur Gazi of Bhaoal, Suna Gazi of Sarail, Mirza Mumin (son of Masum Khan Kapuli) of Chatmohar, Madhu Ray of Khalsi, Binod Ray of Chandpratap, Mazlis Qutb of Fatehabad=Faridpur, and Paloan of Matanga. Satrajit of Bhusana and Raja Raghunath of Susanga sided with the Mughals. Raja Pratapaditya was the zamindar who ruled from Dhumghat and controlled Jessor, Khulna and Bakharganj; and was father in law to Ramchandra of Bakla. (Bakla or Bakherganj including modern Barisal was probably same as the old Chandradvip. Ramchandra was son of Kandarpanarayan, one of the Barobhuyians who ruled from 1584 to 1598 and was the son of the daughter of Paramananda whose mother Kamaladevi was fifth generation from Danujamardan. He married Bindumati, daughter of Pratapaditya, established his capital in Husainpur, and defeated Laksmanmanikya of Bhulua. He was succeeded by his son Kirtinarayan, who was succeeded by his halfbrother Pratapnarayan Ray.) There were also other zamindars like Anantamanikya, son of Laksmanmanikya, of Bhulua and many Pathans, mainly in Sylhet, main among whom was Bayazid Karrani and his associate Khaja Osman, nephew of Qutlu Khan, the last Pathan ruler of Orissa. Also, near Rajmahal, there were Vir Hambir of Mallabhuma and Bankura, Shams Khan in Panchet and Selim Khan in Hijli. Islam Khan, with his gunpowder, horses, and navy, overcame all these zamindars and also defeated Shatrudaman of Kachhar. In 1612, he moved the capital to Dhaka and called it Jehangirnagar. He then captured Kamrup which was then under Pariksit Narayan, an offshoot of the dynasty ruling Coochbehar which also came under Mughal rule. This was the beginning of true Mughal rule in Bengal, a fundamental change in the economic, religious, social, and political structure of Bengal: it was now one of twelve imperial provinces, ruled by outsiders who did not feel native to Bengal but who felt the borders of the empire as economic and cultural frontiers; and which now had sunni ashrafs that did not intermarry with othe Bengalis but rather claimed Iranian ancestry; and with the sufis that brought a pan-Indian religious outlook to the religion of the masses.
The next Subedar was Islam Khan's brother Qasim Khan (1614–7). He again saw revolts from different parts. The next subedar Ibrahim Khan Fatehjang (1617–24) reconquered parts of Bengal, but he was defeated by Prince khurram (shahabu-ud-din, later shah jahan), who had revolted against his father Jehangir. In April 1624, Khurram started ruling independently over Bengal and Orissa, and soon over Bihar and Oudh as well. He was defeated in October 1624, but when Jehangir died in 1627, after a confused period under dâwar bakhsh (1627–28), he started ruling over the Mughal empire as shahabu-ud-din shâh jahân khusraw (1628–deposed in 1657). He defeated the portuguese and recovered hughli in 1632, and fought with Ahom. His son, murad baksh (1657) was defeated by subedar Shuja (1629? 1639?–58) was defeated by another of his sons, dara, who in turn was defeated by Mohy-ud-din Awrangzîb ´âlamgîr (1658–1707) on the Mughal throne. Shuja fled to Arakan and was assasinated.
Mir Jumla (June 1660–died March 1663) was the next subedar of Bengal. During his time, Coochbehar occupied Kamrup, and Ahom, Gauhati. Then Ahom took over Kamrup. Mir Jumla took over both, but both became independent when he died. The next subedar Shaesta Khan (March 1664–June 1688) was known for his economic oppression, but popularity amongst common man, in Bengal. He reconquered Coochbehar, defeated the Arakan and portuguese pirates and conqueured chittagong.
After this, Khan-i-jahan Bahadur was subedar for a year, followed by Ibrahim Khan. Zamindar Shobhasingh and Rahim Singh revolted during his time. In response Aurengzeb sent his grandson Azim-ud-din, known as Azim-us-san (1697–1712), as the subedar. He suppressed the revolt. He let the europeans fortify their settlements and ushered in the modern era in the history of bengal.
Up to history of Muslim Period of Bengal