Jaichand's son, Harichandra continued to occupy Kannauj even after 1193 A.D. The
Muslim supremacy over the kingdom was perplexing or abhorrent to him and so he
discreetly omitted any specific reference to Harichandra or his Muslims
overlord. In 1233-34 Iltutmish ordered the Kannauj Garrison to join the imperial
forces in an expedition against Kalinjar. In 1244, The district of Kannauj was
conferred by the dissolute Alauddin Masaud on his uncle Jalaluddin for his
maintenance. The royal forces reached Kannauj and besieged the fort of
Balsandah. This fortress was very strong and the royal forces returned with
Ghiasuddin Balban, who then possessed the Delhi throne, (1268-87) marched
towards this region and divided the whole area into a number of military
commands. At each of these place he erected forts,garrisoned with seasoned
Afghan troops. Balban himself remained in the vicinity for many months. Ziauddin
Barani writes "Sixty years have passed since these events, but the roads have
ever since been free from robbers." In 1290 Jalaluddin Firoz Khalji visited the
fort of Bhojapur and is believed to have built bridge across the Ganga near the
fort. In 1346-47 Muhammad Tughlaq went on another expedition on to this region
and reach Sargdaori. In 1392, after a gap of about forty five years, this region
was once again up in arms against the imperial authority of this area. In
collusion with the Chauhans and Solankhis of the surrounding tracts, the Rajputs
of this area broke out in open rebellion. In 1394, the suspected outbreak of
another rebellion in this region, the sultan conferred on Khwaja Jahan the title
of Malik-ul-Sharq "and appointed him governor of Hindustan from Kannauj to Bihar
devolving upon him full power." Malik-ul-Sharq died in 1399 and his adopted son,
Mubarak Shah became the virtual ruler at Delhi and reached Kannauj.
In 1414, Khizr Khan (whom Timur had left in charge of his possessions in India)
occupied the throne of Delhi and inaugurated the rule of Saiyid dynasty.
Immediately after his accession in 1423, Mubarak Shah Saiyid marched to Kampil
to suppress the Rajputs of the place.
On Sikandar Lodhi's death in 1517, his son, Ibrahim, became emperor. He reached
Kannauj where he was greeted by Azam Humayun Sarvani, the governor of Kannauj.
The result was that several Afghan chiefs willingly joined and Kannauj became a
fief under the sovereignty of the Mughals. Kannauj appears to have been
recovered by Afghans. In 1527 Babar mobilised his forces against the rebel chief
of Chanderi. Babar now captured Chanderi but lost Kannauj and Shamsabad to the
Afghans. Kannauj became a dependency of the rebels who found themselves at the
head of Muslims and Rajputs. Humayan's continued occupation in the north and
gave the ambitious Sher Shah Suri a free hand to prosecute his designs in the
east. In July 1537, he entrusted the government of Kannauj to his brother-in-law
Nur-ud-din Mohammad. Sher Shah Suri now cut off Humayun's communication with
Delhi while the desertion of Hindal and Nur-ud-din (governor of Kannauj)
completely blocked Humayun from all sides. Humayun fled across the river to
Mainpuri and later in 1543 left India for Kandahar.
It appears that immediately after the capture of Kannauj Sher Shah destroyed the
old city and built a fort of burnt brick there "and on the spot of gaining
victory he built a city Sher Sur." In 1555 the Afghans were over thrown and the
power of the Mughals was once again established by Humayun, who returned India
after 12 years but he died soon in January 1556 and he was succeeded by his son
Akbar. Kannauj was the headquarter of a Sirkar containing 30 Mahals. Kampil,
Saurikh, Sakrawa, Sakatpur and Kannauj of Akbar's time have also retained their
old names except Kannauj. In 1592 Kannauj was given to Muzaffar Hussain Mirza,
but he proved to be a drunkard and was soon deprived.
In 1610, Jahangir (1605-27) granted the government of Kannauj to Abdurrahim, the
son of great Bairam.