Gurudev returned to Kerala again. He underwent regular courses of indigenous and Ayurvedic treatments. Then Gurudev came to the rest-house (vaidika madhom) at Sivagiri Mutt and stayed there. Those who treated him include the reputed Ayurvedic physicians Cholayil Mami Vaidyar, Panappally Krishnan Vaidyar, Thycauttu Divakaran Moos, besides Dr. Krishnan Thampi, Dr. Panikker and Dr. Palpu. The European physician Dr. Noble also treated Gurudev. But Gurudev appeared tired.Those who were with Gurudev at this time have recorded that his cheerfulness and sense of humour did not fade even on his sick bed.

Sree Narayana Guru who was the embodiment of compassion attained mahasamadhi at 3.00 p.m on Thursday September 20, 1928 at Sivagiri Vaidika Mutt.

Sree Guruprasada Swamikal who was with Sree Narayana Guru at the time of mahasamadhi has said the following in his authoritative account of the scene,"By the inevitable law of destiny that great light passed from our sight.

At the time of samadhi Sree Vidynanda Swami was reading Yogavasishtam Jeevanmuktha prakaranam in the presence of Gurudev. "Sree Narayana Gurudevan attained mahasamadhi in a meditative mood, listening to the recital of the section describing the attainment of moksha."

The next day about 6 o'clock in the afternoon Sree Narayana Gurudevan's mortal remains were laid to rest at the top of the Sivagiri hill in the presence of thousands of devotees. The Mahasamadhi Mandir stands there today.

Sree Narayana Gurudev was the incarnation of extraordinary purity of nature, perfect compassion, unwavering idealism, unique karma yoga and celestial genius. As Sri. Moorkoth Kumaran, Gurudevan's grahastha disciple, has recorded in his biography of the saintly guru:

"The world will certainly know the real greatness of that extraordinary saint Sree Narayana Guruswamikal in the days to come when the seed that he has sowed germinates, grows, branches out and blossoms."