They established a planned layout, with the Koniamman temple in the center. From the Cholas, then to the Hoysalas of Karnataka in 1291 . By the early 14th century , the region was ruled by the Muslim rulers of Madurai under the Delhi Sultanate . The Muslim rule in Madurai was ended in the late 14th century by the newly formed Vijayanagara Empire . The Vijayanagara reign brought new settlers from Andhra Pradesh and Karnataka. In the 1550s , the military governors ( Nayaks ) of the Vijaynagara Empire took control of Madurai, with Coimbatore belonging to their territory. After the downfall of Vijayanagara Empire, the Madurai Nayaks established their state as an independent kingdom, with other Vijayanagar offshoots forming new kingdoms in Vellore, Tanjore , Gingee, Chandragiri and Mysore.

The Nayaks introduced the Palayakkarars , who were military governors of their respective regions. By the 1700s , frequent fighting between Madurai and Mysore forces in the Coimbatore region resulted in the egio being ruled by Mysore. At this time Coimbatore was still a village of around 3000 people

In the 1760s , the Mysore throne was usurped in a coup by General Hyder Ali . Ali was hostile to the British , who were gaining a foothold in the area with the help of Arcot Nawab . A series of wars between the British and the Mysore forces continued till Tipu Sultan 's death in 1799 , when the Mysore throne was handed over to the earlier Mysore rulers. At that time the British annexed the Coimbatore region into the Madras Presidency . When Hyder Ali acquired Coimbatore, the population was around 3000.

The village dwindled to 1500 by Tipu's death. Coimbatore played a prominent role in the Second Poligar War against the British in 1801,when the first attack was done against the British Columns stationed in Coimbatore by the Poligars of Salem, Coimbatore and Dindigul region along with some Malabar and Mysore rebels. In 1804 Coimbatore was established as a capital for the newly formed Coimbatore district and in 1848 , it was accorded the municipality status. Sir Robert Stanes , a British entrepreneur and philanthropist, became the first Chairman of the Coimbatore City Council and also founded the Stanes School in 1862,a major higher secondary school that stands till date as a jewel in the crown of the city. In 1981 Coimbatore became a corporation with annexure of the Singanallur municipality.