Shah Jahan ascended the throne in 1628 and assumed the title of Abul Muzaffar Shahbuddin Muhammad Sahib-i Kiran-i Sani. His reign opened with the execution of his brothers and nephews. In the first year of his reign Shah Jahan had to face the rebellion of Jujhar Singh, son of Bir Singh Deo, the Bundela chief who was responsible for murder of Abul Fazl. He made encroachment on the Mughal territory and showed signs of rebellion. Initially he surrendered to the Mughal army but he revolted again in 1635. Later he was pursued by the Mughal troops and killed by the Gonds.
The revolt of Khan Jahan Lodi in 1628 gave much more trouble to Shah Jahan than the Bundela rising. He entered into an alliance with the ruler of Ahmednagar and revolted. Shah Jahan realized the gravity of the situation and decided to personally supervise the operation. But ultimately in 1630 Khan Jahan had to give up & died near the fort of Kalanjar.
With Shah Jahanís accession to the throne, the Deccan policy of the Mughals entered a new phase. Apart from political differences, the Deccan rulers had pronounced Shiahite learnings and were suspected of allegiance to the Shia rulers of Persia. The death of Malik Ambar came as a blessing to the Mughals.
In 1630 his son Fath Kan the minister of Ahmadnagar put the king in confinement and later killed him. In 1631 the Mughal army laid siege on Bijapur but were compelled to raise it after twenty days for lack of provisions. Finally in 1633 the Mughals won the fort of Daulatabad & the Nizam Shahi kingdom came to an end. But Shah Jahanís imperialistic designs could not be satisfied without crushing Bijapur and Golconda. He called upon the rulers of these countries to acknowledge his suzerainty. Abdullah Qutb Shah of Golconda formally recognized the suzerainty of Shah Jahan but the king of Bijapur was not ready to barter away his independence. But ultimately Adil Shah of Bijapur had t acknowledge the over lordship of the emperor & was allowed to retain his ancestral kingdom. Having thus settled the state affairs in the Deccan in 1636 Shah Jahan retired to Agra. Aurangzeb was appointed the Governor of The Deccan & he occupied that post for eight years (1636-44). During this period, Aurangzeb annexed Bagalna near Nasik and reduced the power of Shahji. In 1653, Aurangzeb was appointed the Governor of the Deccan for the second time. He remained in the post till 1657.
In September 1657, Shah Jahan fell ill. The physicians were not hopeful about his recovery. As soon as the news of his illness reached his sons they started making preparations for capturing the throne. In 1658 Aurangzib took over & imprisoned his father. Ultimately in 1666 he did in captivity.
Undoubtedly, Shah Jahan was one of the greatest rulers of the Mughals. The Mughal empire reached its greatest prosperity in the reign of Shah Jahan. As a emperor he led a strenuous life. He personally supervised the minutest details of the administration and appointed men of highest ability as his minister. He was an orthodox musalman but was never unfair to his non-Muslim subjects. He considerably increased the royal retinue, the state-establishments and the magnificence of the court. The Peacock throne, the Taj Mahal, the Agra Fort and numerous other works of architecture and art testify to his wealth as well as his aesthetic sense. He was an excellent calligraphist. His patronage of men of letters and of artisans and craftsmen was in keeping with the traditions of his family. Poetry, music, painting, dancing, astronomy, mathematics and medicine flourished under the generous and intelligent patronage of the emperor.