In the beginning of the Muslim rule, Allahabad was a part of the Delhi Sultanate. Then the Mughals took over from the slave rulers of Delhi and under them Allahabad rose to prominence once again.

Acknowledging the strategic position of Allahabad in the Doaba or the "Hindostan" region at the confluence of its defining rivers which had immense navigational potentials, Akbar built a magnificent fort on the banks of the holy Sangam and re-christened the town as Illahabad in 1575. The Akbar fort has an Ashokan pillar and some temples, and is largely a military barracks. On the southwestern extremity of Allahabad lies Khusrobagh that antedates the fort and has three mausoleums, including that of Jehangir's first wife – Shah Begum. Before colonial rule was imposed over Allahabad , the city was rocked by Maratha incursions. But the Marathas also left behind two beautiful eighteenth century temples with intricate architecture.

In 1765, the combined forces of the Nawab of Awadh and the Mughal emperor Shah Alam lost the war of Buxar to the British. Although, the British did not take over their states, they established a garrison at the Allahabad fort. Governor General Warren Hastings later took Allahabad from Shah Alam and gave it to Awadh alleging that he had placed himself in the power of the Marathas.

In 1801 the Nawab of Awadh ceded the city to the British East India Company. Gradually the other parts of Doaba and adjoining region in its west (including Delhi and Ajmer-Mewara regions) were won by the British. When these north western areas were made into a new Presidency called the "North Western Provinces of Agra", its capital was Agra. Allahabad remained an important part of this state.

In 1834, Allahabad became the seat of the Government of the Agra Province and a High Court was established. But a year later both were relocated to Agra

In 1857, Allahabad was active in the Indian Mutiny. After the mutiny, the British truncated the Delhi region of the state, merging it with Punjab and transferred the capital of North west Provinces to Allahabad, which remained so for the next 20 years.

In 1877 the two provinces of Agra (NWPA) and Awadh were merged to form a new state which was called the United Provinces. Allahabad was the capital of this new state till the 1920s.