The arrival of people from the Central Asian nations such as the Turks and Mongols was a significant turning point in the history of Pakistan. The Qalandars (wandering Sufi saints) from Central Asia, Persia and Middle East preached a mystical form of Islam that appealed to the Buddhist and Hindu populations of Pakistan. The concepts of equality, justice, spiritualness, and secularism of the Sufi strain of Islam greatly attracted the masses towards it. The Sufi orders or triqas were established gradually, over a period of centuries. Pakistan was a place of great cultural and religious diversity. The Muslim technocrats, bureaucrats, soldiers, traders, scientists, architects, teachers, theologians and sufis flocked from the rest of the Muslim world to Islamic Sultanate in South Asia. The Muslim Sufi missionaries played a pivotal role in converting the millions of native people to Islam.

The Mughals were the descendants of Persianized Central Asian Turks (with significant Mongol admixture) and would establish a formidable empire over the breadth of South Asia and beyond. The Mughal Empire included Pakistan and reached as far north as eastern Afghanistan and as far south as southern India. It was one of the three major Islamic empires of its day and sometimes contested its north western holdings such as Qandahar against invasions from the Uzbeks and the Safavid Persians. Although the first Mughal emperor Babur favored the cool hills of Kabul, his conquests would lay the foundations for a dynasty that would hold sway over South Asia for over two centuries. Most of his successors were capable rulers and during the Mughal period the Shalimar Gardens were built in Lahore (during the reign of Shah Jehan and the Badshahi Mosque was erected during the reign of Aurangzeb. However, Aurganzeb was a controversial emperor, who was accused for his persecution of those that refused to convert to Islam. Dangerous criminals were at times set free because they were Muslims. The advent of a tax on Non-Muslims and the forceful conversions of Hindu and Sikh communities in the Pakistan region created laid the building blocks for a region that was going to have a large Muslim majority. Aurangzeb was also known for his desecration and destruction of particular symbolic Hindu temples as well as the execution of the 9th Guru of Sikhism. One notable emperor, Akbar the Great was both a capable ruler and an early proponent of religious and ethnic tolerance and favored an early form of multiculturalism.

Pakistan still bears marvellous architectural monuments built by the Mughal emperors. During the Mughal period, the cities of Delhi and Lahore were made the capitals of the empire. The Taj Mahal and other architectural marvels were the results of the growth of Islamic culture and rule over the South Asia. The Mughals also implemented federal regulations including taxation, social welfare reforms, justice, development of the transport and agricultural system and water canals. The mansabdar system gained prominence during the Mughal Empire and was used to implement a form of ranking military official and landowners throughout the empire and in many ways inspired similar systems in other major Islamic empires of the day such as the Ottoman Empire’s tanzimat reforms.