The paintings of the Nayak phase of Madurai and Tanjavur was as important as the Vijayanagara phase. The traces of Nayaka paintings can be seen at the Tiruparuthikundram apart from the Vijayanagara paintings. Most of these paintings of Nayaka period are of the 16th century and few are from the 17th century.

These Nayaka paintings depict the scenes from the life of Rishabhadeva, the first Thirthankara of Vardhamana, of Krishna, the cousin of the Thirthankara, Neminatha as well as the life of Neminatha himself. These are all graphically portrayed in a long series with elaborate labels in Tamil language giving details of each painting which became the usual feature as such labels are seen in Chidambaram paintings and Tiruvalur etc.

In the Tanjavur temple, there is a long panel facing west, in the circumambulatory passage. This shows Lord Indra on an elephant, Agni (the Lord of Fire) on a ram, Yama (God of Death) on a buffalo, Niritti on a human mount, Varuna (Rain God) on a makara and Marut (Wind God) on a deer. These Nayaka paintings depict the glory of Indra by repeating him on an elephant at one end. These paintings depict the `samudra manthana` scene, showing the rising of the objects from the ocean as it was churned. The things rose shown here include the Kalpavriksha (wish-fulfilling tree), Uchchaisravas (celestial horse), Airavata (heavenly elephant), Kamadhenu (the cow of plenty), Rambha, Urvasi (celestial nymphs) and others. It also depicts Goddess Lakshmi is towards one end on a lotus, with her hands in a posture of assurance of protection and prosperity and is approached by the devatas.

Many other such valuable and noteworthy Nayaka paintings can be seen in various temples of Kumbakonam and other places in Tanjavur district. The Tiruvarurtemple is among the most famous Saivite shrines of South India. One of such paintings of the late 17th and early 18th centuries can be seen on the ceiling, between the rows of pillars in the thousand pillared mandapa. In this painting, the great devotee of Siva, Muchukunda Chola is portrayed as a great friend of Indra and as his great ally in overcoming the asuras. He is shown majestically riding on an elephant in a procession. He is received with great honour by Indra at the entrance of the city and beautiful celestial damsels are shown honouring him from their balconies, which is most beautifully represented.

On the ceiling of the large mandapa of Chidambaram temple, there is a nice Nayaka painting depicting the story of the genesis of the Bikshatana form of Siva and Mohini form of Vishnu. The plan of Siva and Vishnu was to proceed to Darukavana to protect the rishis and rishipatnis (wives of the rishis) by assuming the guise of the naked beggar and the bewitching enchantress. In one of the paintings Ganesa (the elephant faced god) and Umasahita are shown with rishis, Skanda (Muruga) with Valli and Devasena. This painting can be seen towards the other end of the mandapa. Here, one can also see Nandi conversing with Siva and Parvati in Kailasa, Nataraja as Sabhapati with Sivakamasundari (Parvati) surrounded by Ganas dancing and playing musical instruments. These Nayaka paintings here also depict several other stories from Sivapurana, illustrating the lives of saints.

The temple of Tiruvalanjuli has vigorously painted panels depicting Vishnuanugraha Murthi (blessing Vishnu). The story of Muruga teaching Pranava to Brahma and that of Siva with chinmudra is inscribed here. The paintings of the Nayaka period continue the traditions of the Vijayanagar craftsmen and they influenced the art of Mysore, Vellore, Penukonda and Srirangapattinam.