The organisation clinched news headlines in 2007-08 after its members and its affiliated organisation the Hindu Janjagruti Samiti were arrested for their alleged involvement in a series of bomb blasts in Mumbai and Goa. In the following years, police investigation found members of the Sanstha to be key conspirators in the murders of rationalist thinkers Narendra Dabholkar, Govind Pansare, Gauri Lankesh and M. M. Kalburgi. Sanatan members allegedly planned to eliminate the intellectuals allegedly for the criticising and mocking Hindu religion.

According to Sanstha’s website, the headquarter in Goa is a model of Hindu Rashtra and home to 400 sadhaks or permanent followers. Around 1000 odd sadhaks stay in other locations in Maharashtra. It conducts spiritual congregations for adults and also trains young children between the age group of 5-15 years in Balsanskar classes. The Sanstha is known to impart knowledge on Hindu dharma, spirituality, nationalism and patriotism. It teaches followers to raise voice against "mockery of Hindu religion, deities, scriptures and saints".

Not much is known about the workings of the organisation or its religious teachings due to strict secrecy followed by full time followers. The views and ideology of Sanatan Sanstha is however evident in the inhouse newspaper called Sanatan Prabhat. The newspaper is widely circulated in Maharashtra and covers news and issues related to “protection of nation and Dharma” in Marathi. It also runs a Spiritual Science Research Foundation for advancement of spirituality and has several foreign nationals as followers.

The organisation has made several bizarre claims on spirituality and divine powers of its founder Dr Athavale, an alumni of Grant Medical College in Mumbai. It is claimed that Athavale displays several divine signs, purportedly due to his connection with divine consciousness. These include appearance of symbol Om on his forehead, and pillow cover and pink marks on his shirt. Similar auspicious signs have also appeared on other devoted Sadhaks. The Sanstha provides several set of instructions to followers to attain high levels of spirituality through the

conduct of daily activities like bathing, hair style, eating, praying in a “spiritually scientific” manner.

Calls to ban the Sanstha have been periodically raised, yet it has managed to avoid direct action and has been cleared by courts. Operating covertly, it functions in 17 states with restricted access limited to full-time members.

The recent judgement in Dabholkar’s murder case, failed to indict key conspirators from the Sanstha despite evidence gathered by the CBI and Pune police. Earlier this month, Pansare’s family alleged negligence by investigating agencies and offered evidence on the Maharashtra ATS against Sanstha’s criminal links in the murders of rationalists. They have demanded the state authorities to investigate the Hindu extremist organisation and identify the real masterminds.