The medieval period starts with the Bhakthi form of Hinduism in 1000 A.D. and in its first part of 400 years saw the piece-meal conquest of Muslim invaders, the establishment of the Moghul empire and the decline of Rajput power. The later Chalukya were ruling in Deccan and Cholas were in Tamilnadu. Vijayanagar empire came to power at this time. While the religious persecution destroyed the practice of rituals and the Temple worship in the North, inter-group rivalry among kings in the South invited the Muslim rulers to assist them and ultimately take over the land. Many Temples in the South were looted by the occupying forces and were destroyed of all wealth and architecture. The Visishta-advaitham of Sri Ramanuja Acharya and Dvaitham of Sri Madhva Acharya forms of devotional Bhakthi system of Vaishnavism and belong to this time. This period also saw the rise of Saiva Siddhantha and Veera Saiva systems. With these changes in the practice, teachings of Buddhism were absorbed and the spread of also Jainism declined. The Vedic commentaries of Sayana, Jayadeva's Gita Govinda, and Sarnga Deva's works on Music 'Sangitha Ratnakara' and in South India Kambar's Ramayanam and Sekkizhar's Periyapuranam in Tamil belong to this age.

Many great Temples of the South India were built during this time. The famous Chola bronzes, Nataraja, Nepal and Tibet bronzes, Sculptures of Konarak and Puri and the Hoysala architecture of Mysore are famous in this period. Vaishnavite Saints Ramanuja, Madhva and Vedantha Desika belong to the later period of this age. Whereas the rise of Buddhist and Jain influence gave rise to Sri Sankara's Philosophy and Advaita theory in the previous age, the arrival of Islamic thoughts, Moghul rule and Judo-Christian influence gave rise to the popularity and the rise of Bhakthi form of Hinduism, group prayers and the Dvaitha and Visishta-advaitha Theory of Sri Madhva and Sri Ramanuja. Similarly Islamic influence and Mogul rule later gave rise to the reform movements of Chaitanya, Kabir and Guru Nanak. This was the beginning of Judeo-Christian influence, by those who came as refugees, and later as traders and rulers.