The tyrannical rule of the last abyssinian sultan of bengal was ended by his minister hussain shah who ruled as alauddin hussain shah (1493–1519) and founded the hussain-shahi dynasty. Many stories abound of his intrigues which led him to be the king, and he is supposed to have established law and order in his new kingdom by harshly killing many people, and amassing large amount of wealth. He replaced the pAikas, the palace guards, who were responsible for previous assassinations, and removed the abyssinians from his kingdom to gujarat and south India. In addition to Bengali Hindus, his high officials were mainly chosen from the Sayyids, Mughals, and Afghans. However, he was not very liberal towards the hindus: not only did he destroy hindu idols in wars, but opression of hindus was also widespread during his times, though he himself may not have been directly responsible for it, and often turned a blind eye to hindu practices around him; it is also to be noted that during his time, a large number of Hindus converted to Islam to gain positions and social advantage. He moved his capital from gauD.a to ekDAlA. He extended his kingdom to cover large parts of Bihar and Assam as well; though it is a small gain in relation to his continuous wars. Not only did shrI caitanya live during his time, Bengali art and culture also flourished; though it is not clear whether he explicitly supported such activity.
He was followed by nasib shah who ruled as nasir-ud-din nusrat shah (1519–assassinated in 1533), who was allowed to issue his own coinage since 1516. He is supposed to have had good relations with his brothers even after coming to power. According to tradition, in 1527, he appointed his sister's husband, Makhdum Alam, to conquer trihut completely after killing its ruler kaMsanArAYaNa. Around 1521, the Delhi Sultanate, then under Ibrâhîm Lôdî (1517–1526), weakened and the local governors, many afghans of lohAnI and farmulI dynasties, became independent in the region around Bihar. Finally, in 1526, the mughal ruler (al-ṣultānu 'l-ʿazam wa 'l-ḫāqān al-mukkarram pādshāh-e ghāzī) Zahir al-Din Muhammad (ﻇﻬﻴﺮ ﺍﻟﺪﻳﻦ محمد) Bâbur (b. Feb 23, Feb 14 before the calendar reform, 1483–d. Dec 26, 1530; son of Qutluq Nigar Khanum (daughter of Yunus Khan, ruler of Moghulistan and descendant of Chagatai Khan, son of Genghis Khan) and ‘Umar Shaikh (Mirza) Shah, ruler of Fergana Valley and son of Sultan Abu Sa’id Shah, son of Sultan Mahmud Shah, son of Mirza Miran Shah, son of Amir Timur bin Taraghay Barlas Gurkani), who lost his state ferghana and found a new state in Afganisthan, won the first battle of Panipat and ended Afghan rule in Delhi; Babar soon conquered all the way upto Bengal border. The dynasty he founded was called Sultanat Gârkani (گوركانى) after the title (Persianized form of Mongolian kürügän meaning son-in-law) taken by Amir Timur in 1370 on his fourth marriage, to Saray Mulk Khanum, daughter of Qazan of Mawarannah, son of Yasa'ur, son of Chübei, a great-grandson of Chagatai Khan. The dynasty later considered themselves Chugtai (چغتائی), and today are usually referred to as Sultanat Mughal (مغولی), the Persianized form of Mongolian Mongol.
Nusrat Shah gave refuge to the afghan nobles displaced from Delhi and married a daughter of ibrahim lodhi. When the lohani chief Bahar Khan, ruler of Bihar, died, his infant son Jalal Khan was defeated by Ibrahim Lodi's brother, Mahmud, who then took over Jaunpur. South Bihar was under the governorship of Sher Khan. The Afghans attacked Babar, though Sher Khan soon accepted Mughal dominionship over him; Nusrat Shah tried to stay out of a direct conflict. He was not completely successful, but ended with a treaty with Babar. Nusrat Shah's general Hamza Khan, ruler of caTTagrAma, had to fight against devamANikya of tripurA. In 1532, Bengal fought against the kingdom of ahom. He allowed portuguese to trade and expelled them when they burnt chittagong. He built numerous mosques like sonA masjid of gauD.a. Coochbehar might have become independent under him.
He was followed by his son ala-ud-din firuz shah II (1533). Before becoming the sultan, he had the poet shrIdhara kavirAja compose kAlikAmaGgala or vidyAsundara. He fought a war against Ahom. Within a year, he was killed by his uncle Ghiyas-ud-din Mahmud.
Abdul Badr, also known as Abd Shah and Badr Shah, probably revolted during Nusrat Shah's reign. He later assasinated Firuz Shah and ruled as Ghiyas-ud-din Mahmud Shah (1533–38). He lost the battle against the Assamese, and because of the Assamese and Koca pressure, left kAmarUpa as well. He initially treated the portugese very badly, but finally let them establish two settlements in caTTagrAma and saptagrAma. During his time, Delhi was under Naseer-ud-din humâyûn (1530–1540). In Bihar, Sher Khan was becoming more powerful. Ultimately, Sher Khan sacked gauD.a in 1537 and won over both Bengal in 1538 and Delhi in 1540. The poet vidyApati probably was an official in Mahmud Shah's government.