Ala-ud-din Khilji, the second ruler of the Khiliji Dynasty, attacked the Mongol Empire in 1299. The Khilji army led by Zafar Khan easily defeated the Mongols and forced them to retreat. Zafar Khan pursued them but Mongol general Qutlugh Khwaja played a trick on him where he was surrounded by the Mongols and was eventually killed. Ala-ud-din Khilji however, continued his attacks on them that drove them away to the place from where they had descended.
It took a long time for the Mongols to re-organise themselves and prepare for an attack. They waged a war on Ala-ud-din Khilji at a time when the later was engaged in besieging Chittor. With an army of almost 12,000 under the leadership of Targhi, the Mongols travelled to Delhi and made a surprise attack. The governors could hardly restrain their attack and could not even send their forces in time. The series of invasion forced Ala-ud-din to withdraw to Siri for almost two months. In the meanwhile the Mongols invaded and plundered Delhi and its surrounding areas.
Ala-ud-din Khilji still had the Siri Fort under his possession. He fortified his forts along the borders and equipped them with a strong force. Besides this, new fortifications were also constructed for protection of the area. New forces led by special governors were formed with the aim to guard the border areas. However, these strong measures could not hold back the Mongol army. The forces under the headship of Ali Beg and Tartaq intruded into the premises of Punjab as well as in the neighbourhood of Amroha. They completely ransacked Punjab and destroyed everything on their way.
Ala-ud-din Khilji nonetheless, did not give up in this mission. He soon formed a strong army under Ghazi Malik and the famous Malik Kafur, his two tough generals and sent them to fight the invaders. The Khilji forces made a surprise attack on the Mongols and in the Battle of Amroha captured Kubak and other Mongol generals. They were produced in front of Ala-ud-din Khilji who had them trampled by elephants. The heads of other Mongol prisoners, who were put to death, were hung on the fort walls.
The Mongols with their left forces under the leadership of Kebek marched towards Himalaya Mountains crossing the Indus River near Multan. They were seized by Ghazi Malik, the governor of Punjab who also captured almost 50,000 Mongols including a general of the Mongol army. By order of Ala-ud-din Khilji they were all put to death.
In 1307-1308 the last Mongol invasion of the period took place under the leadership of Iqbalmand and Tai Bu. The forces were on the verge of crossing the Indus Valley when they were captured by the Khiljis and killed. After the death of Duwa, the Mongol Khan, the clash over the succession subdued the flurry of Mongol raids in India.
Ala-ud-din Khilji, known to be an efficient strategist effectively planned his actions and sent a strong army under the expert general Ghazi Malik to Ghazni, Kandhar and Kabul. The series of attacks completely destroyed the Mongol army heading towards India. The Khilji also took Warangal, Siwana and Jalor into their possession. The army now under Commander Malik Kafur attacked Malababar from Devagiri in 1311 and amassed huge wealth. The Khilji king soon got a hint that the Mongol captives who were converted to Islam at the order of the King were planning a secret attack on him. He thus, had almost 20,000 arrested and put to sword. The court of Delhi is also said to have killed the emissaries of Oljeitu.
The Mongols next attacked when the Tughluq Dynasty had overpowered the Khiljis. The Chagatai Mongols in 1327 annexed the frontier towns of Lamghan and Multan under the leadership of Tarmashirin. The Tughlaq ruler in order to safeguard his dynasty paid a huge amount to the Mongols. Further no other large scale Mongol attacks took place in India excepting small Mongol forces waging wars on the local powers in the north western region.