Shah, accompanied by BDJS supremo Thushar Vellappally and former BJP state president V Muraleedharan, visited the hillock mutt, located about 50 km from here, after attending a set of crucial party leadership meetings in the state capital.
He offered obeisance at the maha samadhi mandapam, the final resting place of the Guru and met veteran swami Prakashananda, President of Sree Narayana Dharma Sangham Trust.
Shah later went round its sprawling campus and visited the Vaidika Mutt, a more than 100-year-old building where Mahatma Gandhi and Rabindranath Tagore had met the Guru.
Later he lunched with the sanyasis and held brief discussions with them, party sources said.
Prime Minister Narendra Modi visited the Mutt last year.
Established by Narayana Guru who propagated the message of "One Caste, One Religion and One God for Mankind", the Sivagiri Mutt is a major spiritual-cum-pilgrim centre of the backward Ezhava community in Kerala.