The Emperor Jahangir was a capricious despot, addicted to alcohol and opium, whose ambition for the throne caused him to rebel against his father and imprison and blind his son. He could not trust his other sons or his nobles. The Timurid emperors maintained large harems. Akbar had 5,000 women in his harem with many of his wives taken for political purposes to create alliances. Jahangir considered himself a connoisseur and collected women for their beauty. In Mughal India, women became marriageable and sexually active upon puberty. By the age of thirty, they were considered past their prime. Jahangir realized his own limitations and his need for a trusted consul who would not pose a danger to his power. He turned to the capable thirty-five year old Mihrunnisa to fulfil this role. She was declared Empress in 1611 at the Red Fort in Agra. They had no children together. She proved a capable governing partner, ruling the kingdom and protecting his throne especially during the periods when he was indisposed through addiction or illness. She struck coins and sent royal commands in their joint name, a rare phenomena in the male dominated Islamic political power structure.

Mihrunnisa was the daughter of a well-educated Persian official, who having suffered a reversal of fortunes in his own country, decided to migrate to Mughal India with his family in 1577. They joined a caravan on its way to India but had the misfortune of being robbed along the way. They were in such dire straits that when Mihrunnisa was born, they considered abandoning her. Eventually, through the kindness of the caravan chief, the family including Mihrunnisa reached Agra intact. Educated Persian officials were in demand in Akbar's court and her father secured an appointment. He must have performed his duties well as he was soon appointed the Imperial treasurer in Kabul.

Mihrunnisa would have visited Agra several times and tradition has it that Prince Salim (the future Jahangir) was enchanted by her. He was known for his roving eye and lack of restraint. He had a liaison with one of his father's favourite concubines, Anakali, that led to the execution of the unfortunate beauty. In 1594, the growing interest of Salim in the seventeen-year-old Mihrunnisa, induced Emperor Akbar to betroth her to a successful Persian adventurer, Sher Afghan, who had performed good service during a military campaign.