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Conquest of northern India

Around the same time, Alauddin turned his attention towards the present-day state of Rajasthan to subdue the Rajput kingdoms for a secure base to Gujarat and Malwa and for further expeditions in the South. In 1299 CE, Alauddin besieged the fortress of Jaisalmer ruled by Bhatis at the time under Jait Singh I. Following a long siege and due to the dearth of food and resources, eventually, the besieged Rajputs under the command of Mularaja performed Saka where the women committed Jauhar and the men fought until death. Thus, Alauddin successfully penetrated into territories of the Bhattis. After the conquest of Jaisalmer, it remained under the Khalji's for few more years.

In 1301, Alauddin ordered Ulugh Khan and Nusrat Khan to invade Ranthambore, whose king Hammiradeva had granted asylum to the leaders of the mutiny near Jalore. After Nusrat Khan was killed during the siege, Alauddin personally took charge of the siege operations, and conquered the fort in July 1301. During the Ranthambore campaign, Alauddin faced three unsuccessful rebellions. To suppress any future rebellions, he set up an intelligence and surveillance system, instituted a total prohibition in Delhi, established laws to prevent his nobles from networking with each other, and confiscated wealth from the general public.

In the winter of 1302–1303, Alauddin dispatched an army to ransack the Kakatiya capital Warangal. Meanwhile, he himself led another army to conquer Chittor, the capital of the Guhila kingdom ruled by Ratnasimha. Alauddin captured Chittor after an eight-month long siege. According to his courtier Amir Khusrau, he ordered a massacre of 30,000 local Hindus after this conquest. Some later legends state that Alauddin invaded Chittor to capture Ratnasimha's beautiful queen Padmini, but most modern historians have rejected the authenticity of these legends.

While the imperial armies were busy in Chittor and Warangal campaigns, the Mongols launched another invasion of Delhi around August 1303. Alauddin managed to reach Delhi before the invaders, but did not have enough time to prepare for a strong defence. Meanwhile, the Warangal campaign was unsuccessful (because of heavy rains according to Ziauddin Barani), and the army had lost several men and its baggage. Neither this army, nor the reinforcements sent by Alauddin's provincial governors could enter the city because of the blockades set up by the Mongols. Under these difficult circumstances, Alauddin took shelter in a heavily guarded camp at the under-construction Siri Fort. The Mongols engaged his forces in some minor conflicts, but neither army achieved a decisive victory. The invaders ransacked Delhi and its neighbourhoods, but ultimately decided to retreat after being unable to breach Siri. The Mongol invasion of 1303 was one of the most serious invasions of India, and prompted Alauddin to take several steps to prevent its repeat. He strengthened the forts and the military presence along the Mongol routes to India. He also implemented a series of economic reforms to ensure sufficient revenue inflows for maintaining a strong army.

In 1304, Alauddin appears to have ordered a second invasion of Gujarat, which resulted in the annexation of the Vaghela kingdom to the Delhi Sultanate. In 1305, he launched an invasion of Malwa in central India, which resulted in the defeat and death of the Paramara king Mahalakadeva. The Yajvapala dynasty, which ruled the region to the north-east of Malwa, also appears to have fallen to Alauddin's invasion.

In December 1305, the Mongols invaded India again. Instead of attacking the heavily guarded city of Delhi, the invaders proceeded south-east to the Gangetic plains along the Himalayan foothills. Alauddin's 30,000-strong cavalry, led by Malik Nayak, defeated the Mongols at the Battle of Amroha. Many Mongols were taken captive and killed; the 16th-century historian Firishta claims that the heads (sir) of 8,000 Mongols were used to build the Siri Fort commissioned by Alauddin.

In 1306, another Mongol army sent by Duwa advanced up to the Ravi River, ransacking the territories along the way. Alauddin's forces, led by Malik Kafur, decisively defeated the Mongols. Duwa died next year, and after that the Mongols did not launch any further expeditions to India during Alauddin's reign. On the contrary, Alauddin's Dipalpur governor Malik Tughluq regularly raided the Mongol territories located in present-day Afghanistan.