According to contemporary historians, Akbar took a great interest in the building of Fatehpur Sikri and probably also dictated its architectural style. Seeking to revive the splendours of Persian court ceremony made famous by his ancestor
Timur, Akbar planned the complex on Persian principles. But the influences of his adopted land came through in the typically Indian embellishments. The easy availability of sandstone in the neighbouring areas of Fatehpur Sikri also meant that all the buildings here were made of the red stone. The Imperial Palace complex consists of a number of independent pavilions arranged in formal geometry on a piece of level ground, a pattern derived from Arab and central Asian tent encampments. In its entirety, the monuments at Fatehpur Sikri thus reflect the genius of Akbar in assimilating diverse regional architectural influences within a holistic style that was uniquely his own.
The Imperial complex was abandoned in 1585, shortly after its completion, due to the exhaustion of the small, spring-fed lake that supplied the city with water, and its proximity with the
Rajputana, with which the Mughal Empire was often at war. Thus the capital was shifted to
Lahore so that Akbar could have a base in the less stable part of the empire, before moving back to Agra in 1598, where he had begun his reign as he shifted his focus to
Deccan. In fact, he never returned to the city except for a brief period in 1601. In later Mughal history it was occupied for a short while by the Mughal emperor
Muhammad Shah (1719 -1748) and his
Sayyid Hussain Ali Khan Barha, one of the
Syed Brothers, was murdered here in 1720. The palaces were occupied by the
Marathas after their conquest of Delhi, then transferred to the British army, which used the fortified complex as a headquarters and barracks. Restoration began under Lord Curzon.
Because the palace area has been in nearly continuous use over the centuries, much of the imperial complex which spread over nearly two mile long and one mile wide area is largely intact. It is still surrounded by a five mile long wall built during its original construction on three sides. However, apart from the imperial buildings complex and the magnificent mosque which continues in use, little of the city survives. The former site of the city is mostly barren, except of ruins of the
bazaars of the old city near the
Naubat Khana, the 'drum-house' entrance at Agra Road. The modern town lies at the western end of the complex, which was a municipality from 1865 to 1904, and later made a
notified area and in 1901 had a population of 7,147. For a long time it was still known for its masons and stone carvers, though in Akbar time it was known and 'fabrics of hair' and 'silk-spinning'. The village of Sikri still exists nearby.
Basing his arguments on the excavations by the
Archaeological Survey of India (ASI) in 1999-2000 at the Chabeli Tila, senior
Agra journalist Bhanu Pratap Singh said the antique pieces, statues, and structures all point to a lost "culture and religious site," more than 1,000 years ago. "The excavations yielded a rich crop of Jain statues, hundreds of them, including the foundation stone of a temple with the date. The statues were a thousand years old of Bhagwan Adi Nath, Bhagwan
Rishabh Nath, Bhagwan
Mahavir and Jain Yakshinis," said Swarup Chandra Jain, senior leader of the
. Historian Sugam Anand states that there is proof of habitation, temples and commercial centres before Akbar established it as his capital. He states that the open space on a ridge was used by Akbar to build his capital.
 A 400 sq-m mound was opened near the village of Nagari, some half a kilometre from the ramparts of the 16th century fort, a sandstone chamber was found, filled with decapitated and broken idols of Jain
The place was much loved by
Babur who called it as Shukri ("Thanks"), for its large lake of water needed by the Mughal armies.
Annette Beveridge in her translation of
Baburnama noted that Babur
points "Sikri" to read "Shukri".
 Per his memoirs, Babur constructed here a garden called the "Garden of Victory" after defeating
Rana Sangha at its outskirts.
Gulbadan Begum's Humayun-Nama describes that in the garden he built an octagonal pavilion which he used for relaxation and writing. In the center of the nearby lake, he built a large platform. A
baoli exists at the base of a rock scarp about a kilometre from the
Hiran Minar. This was probably the original site of a well-known
epigraph commemorating his victory.