In a dispute that arose over the succession to the Pandya throne, one claimant appealed for help to emperor Ala-ud-din of Delhi, whose general, Malik Kafur was attacking various kingdoms in South India. In 1310. Malik Kafur marched into Madurai.
Malik Kafur returned to Delhi following after the event. The Pandyas protested the invasion, which continued for a few years in spasmodic fashion. The weakness of the Pandya regime caused the neighboring Chera ruler to invade and defeat the Pandya ruler, and he crowned himself in 1313.
But muslim rule was soon re-established at Madurai, ruling Madurai, Trichinopoly and even South Arcot. Madurai was annexed to the empire of Delhi during the reign of Sultan Ghiyathuddin Tughluq by about 1323 A.D. For the next 48 years, Madurai was under muslim rule, first as a feudatory of the Delhi Sultanate and later under independent sultans. In 1333, during the rule of Muhammad bin Tughlaq, Ala ud din Ahasan Shah declared independence from the Delhi sultanate and ruled the area until he was killed by one of his officers in 1339. Alaud din Udauji Shah (AD 1339-1340) took power in 1339, but soon met with the same fate. Qutb ud din Firoz (AD 1340) took over in 1340 and was killed in about forty days. Giyaz uddin Muhammad Damghan (AD 1340-1344) ascended the throne in 1340 and later married a daughter of Ahasan Shah. Ibn Batuta visited Madurai during his reign and he testifies to his atrocious behaviour. He was defeated initially by the Hoysala Veera Ballala, but he later captured and killed Ballala. He died in 1344. Nazir ud din Mahmud Damghan (AD 1344-1356), Adl Shah (AD 1356-1359), Faqr ud din Mubarak (AD 1359-1368) and Ala ud din Sikandar (AD 1368-1377) followed him in succession.
Kampana Udaiyar, a Vijayanagar prince and an agent of Bukka Raya who also served as a General in the Vijayanagar army, marched into Madurai in 1372. He expelled the Muslim sultan, Sikandar out of Madurai. Sikandar was totally defeated in 1377. The region became part of the Vijayanagara Empire. The conquest of the Madurai Sultanate was complete in 1378, when Harihara Raya declared himself as the "Emperor of the South".