The second battle of Tarain in 1192 A.D. dies not appear to have brought the region comprising the present district of Ballia under the immediate sovereignty of the Muslims. With the defeat and death of Jaichandra in the battle of Chandawar in 11.93, at the hands of Shihab-ud-din Ghuri, almost all of northern India lay at his feet but the effect of his conquest in the early years of his reign over this region appears to have been insignificant. This is evidenced by the comparative absence of Muslim remains in the district and also by the manner in which the Rajputs were left in apparently undisturbed possession.

The Muslim forces seldom appeared beyond the Saryu river and the tract on the east of that river remained practically in the hands of the Rajputs. the earliest being the Sengars. Dikhits, Kinwars. Nikumbhas. Naraunis, Barwars, Karchokias and Lohatameas, all are of the same period. Later they were driven eastwards, apparently owing to the Muslim pressure on the west. That the tract remained unconquered may by ascribed to its geographical position and remoteness.

Muslim names of places are rare in this district and references to it in the histories of Muslim historians less common. The was probably the result of the absence of Muslim proprietors at that time, those that remained being in most cases the dependents of local qazis and kanungos whose offices were hereditary during Muslim rule and who resided in the towns.According to tradition, pargana Sikandarpur was colonized by Muslims. It is believed that Qutib-ud-din Aibak, Muhammad capture of Varanasi on his way to Bihar and that he erected a fort on the place now known as Qutbganj on the banks of the Ghaghra.

The village of Kathaura or Kathanda, in pargana Sikandarpur east of the Bansdih tahsil, was divided into two parts, one being called Kathaura and the other Qutbganj. A mound is still visible there of which it is believed that it constitutes the ruins of a fort built in the time of Qutb-ud-din Shah. The name of this sultan is preserved in that of the hamlet of Qutbganj which stands on the banks of the Ghaghra a short distance north of the main site.Meanwhile Ikhtiyar-ud-din Muhammad, son of Bakhtyar of the Turkish tribe of Khalj, had received some fiefs between the Ganga and the son, then took Tirhut and invaded Bihar capturing its capital. In his march he must have penetrated the district of Ballia and is certain that it was included in the territory of Bengal and Bihar in 1202 and hat the town of Kathaura (on the banks of the Ghaghra) had been in communication with he Muslim principalities of Bengal. Thus the district of Ballia passed under the sway of the Muslim.

The tract occupied by the present district of Ballia finds no mention in the history of mediaeval India written by Muslim historians probably because the surrounding areas of Ghazipur. Jaunpur and Saran (in Bihar) remained in the possession of Hindu proprietors till the beginning of the reign of Muhammad Taughlak (1325). At certain periods the district was actually subjected to the Muslim rulers of Bengal. In 1377. when Firoz Shah returned from eastern Bengal, he placed Jaunpur under Malik Bahroz Sultana and Bihar under Malik Bir Afghan, who reduced the Hindus to complete subjection. The district of Ballia was also placed in the charge of these two persons till the death of Firuz Shah after which they increased their own power at the expense of the central authority till 1394, when Khwaja-i-jahan, the vizier of the kingdom, was deputed to the charge of Jaunpur with full control over the territory extending from Kannauj to Bihar, including the district of Ballia. He made Jaunpur an independent Muslim kingdom and it remained as such from 1394 to 1479 during which time at least a part of the tract included in the present district of Ballia came within its sway which, according to an inscription on a black marble slab fixed in wall of a tomb at Kharid, extended eastwards as far as Bihar.

The tract covering the present district of Ballia appears to have remained under the undisputed control of the Jaunpur kingdom till 1479 when Buhlul Lodi defeated Sultan Husain, its last ruler, and obliged him to flee to Bihar.According to a legend, Kharid (a small village in pargana Sikandarpur) was given its name by the king of Bengal (Abu Muzaffar Sultan Husain). It was he who ruled over Bengal in 1495. An inscription on a stone slab found near Kharid mentions the king's name and the name of Kharid was under the Muslim ruler of Bengal.

Sikandarpur, in the pargana of the same name in tahsil Bansdih, was founded by Sikandar Lodi and named after him, towards the end of the 15th century, though it is also said that it was founded by one of his officers. He is also said to have erected a fortress at this place. From the time of Qutb-ud-din Aibak (or about the beginning of the 13th century) Muslim immigrants began to arrive in the district, probably from the Muslim principalities of lower Bengal and gradually established their ascendancy throughout the northern part of pargana Sikandarpur having ousted the Hindu proprietors of the place.After the defeat of Husain Shah, Buhlul pursued him as far as the confines of Bihar. When Bauhlu reached the town of Haldi (in this district) he heard the news of the death of Qutb Khan Lodi, his cousin. After observing the days of customary mourning, he returned to Haunpur which he left in the possession of Barbak. After Buhlul's death, Barbak became an independent king and a potential danger to his brother, Sikandar, Lodi, who succeeded Buhlul in 1488 as the sultan of Delhi.

In 1493 the district of Ballia was affected by an extensive Hindu rebellion in the wake of which Barbak was driven out of Jaunpur but was reinstate when Sikandar Lodi returned. Sikandarpur was garrisoned but whatever importance it attained during the days of the Lodis appears to have waned under the Mughals, when no imperial were maintained or deemed to be necessary in these parts.When Babur defeated Ibrahim Lodi at Paniput in 1526 and became the ruler of Delhi, the Afghan nobles of the east strengthen their power within a short time. From an inscription on a black marble slab found near the Ghaghra and later fixed in the wall of the tomb of Rukn-ud-dib at Kharid, it appears that a mosque was built at Kharid in 1527 during the days of Nusrat Shah, an independent king of Bengal. This inscription, which is in Tughra characters, confirms that Nusrat Shah had extended his authority over the whole of northern Bihar and as Karid lies on the right bank on the Ghaghra, Nusrat Shah must have held sway temporarily in Azamgarh in which part of the present district of Ballia lay.

The name of the sovereign of Vengal would not have occurred had Muhammad Shah exercised real authority over this region and at this time Kharid seems to have been in the possession of the sultan of Bengal According to tradition, the town of Kharid was then known as Ghazanfarabad, a magnificent city extending for a considerable distance between Sikandarpur and Turtipar.In 1528 Babur marched eastwards knowing that Nusrat Shah had encroached on Bihar. The Afghans under Mahmud (Sikandar Lodi's son) reached the north bank of the Ghaghra while Babur reached Ghazipur by the Ganga and then went on to Chaunsa, touching the border of the district as well. He sent his artillery into Doaba to contain the enemy by bombardment and dispatched Mirza Askari through Ballia with instruction to cross the Ghaghra at Haldi and to threaten the Afghans on their right flank, he himself crossing over just below the confluence.

Nusrat Shah. who had joined Mahmud, separated from his forces and withdrew the army of Kharid, as it was called. Babur attacked and defeated the Afghans, driving them across the Ghaghra in the direction of Luck-now and, keeping to the north bank of the Ghaghra, he went on pursuing them. After Babur's death the Afghans set up Jalal-ud-din Lahani, Mahmud's son, as their sovereign and all the defeated Afghans allied themselves with him, chief among them being Farid Khan Suri, better known as Sher Khan and afterwards as Sher Shah. The district continued to remain under to control of Delhi during the reigns of Sher Shah and of his successor, Islam Shah. When Akbar came to the throne (in 1556) the east, in which was included the district of Ballia, was conquered in 1559.

About 1565, Ballia was affected by the rebellion of Khan Zaman against Akbar. The records of Akbor's reign in the Ain-i-Akbari furnish a certain amount of information regarding the condition of Ballia in respect of cultivation, the revenue and the principal landholders of each pargana. The district lay party in the sirkar of Ghazipur and the remainder, with the exception of Doaba, in the sirkar of Jaunpur, Both these sirkars were included in the subah of Allahabad, Doaba was not a separate pargana but formed a portion of sirkar Rohtas in the Subah of Bihar.

It is not possible to determine the revenue then paid in Doaba. The district paid a revenue of Rs.1,55,000 on a cultivated area of 80,200 acres. The revenue demand was extremely high. At a conservative estimate, the purchasing power of the rupee in Akbar's days was probably at least eight times as great as what obtained of the 20th century.The name of the parganas (with the exception of Doaba) remained unchanged. There were three mahals (revenue paying units) of the present district of Ballia in the sirkar of Jaunpur, namely Kharid.

Sikandarpur and Bhadaon. Kharid, a prosperous pargana, was then held by Kausik Rajputs, It had a cultivated area of 30,914 bighas and paid a revenue of 14,45,743 dams (absolute Indian copper coin, one fortieth of a rupee) and contributed a contigent of 50 horsemen and 5,000 foot.Sikandarpur, a pargana which lay in the sirkar of Jaunpur, was somewhat larger than at present, as four tappas (tracts of land) were afterwards transferred to Azamgarh, though, the loss was compensated for to some extent by the addition of tappa. Dhaka from Zahurabad and Shah Salempur from Kopachit.

The leading zamindars were Brahmansa, as the Baid had not yet asserted their supremacy, the date of their advent being 1628. The military contingent was 10 mounted men and 3,000 infantry and the revenue 17,06,417 dams on about 32,514 bighas of cultivation.The mahal of Bhadaon had 43,000 bighas under cultivation the revenue being 2,29,315 dams and the zamindars Siddiqi Sheikhs, who provided 10 horse and 100 foot.There were four mahals in the Ghazipur sirkar, namely Ballia, Kopachit, Lakhnesar and Garha. In all these parganas, except Garha, t he zamindara were Rajpurs. Garha was the property of Brahmanas or of Rajputs. Ballia had about 28,344 bighas under tillage, paid a revenue of 12,50,000 dams and contributed 200 cavalry and 2,000 foot.

In Kopachit there were about 19,266 bighas under cultivation and the revenue was 9,42,190 dams, the local contingent being 20 horse and 2,000 foot. The Akbari gives the details about pargana Lakhnesar which had approximately 2,883 bighas under cultivation, the revenue being 1,26,636 dams. Garha, which furnished 200 foot, had 10,049 bighas under cultivation and paid a revenue of 5,00,000 dams