Seven ashram office bearers were booked in connection with the murders of Abhishek Vaghela (11) and his cousin Dipesh Vaghela (10). The boys went missing from a residential school of his ashram in Ahmedabad in April 2008. Their decomposed bodies were later found on the banks of the Sabarmati a few days later. The post-mortem report revealed that all their internal organs were missing. Asaram was accused of murdering two four-year-old students of his school at Chhindwara in Madhya Pradesh.

Asaram has also been charged with grabbing huge tracts of land illegally all over the country. The Gujarat Government acknowledged in February 2009 that his ashram had encroached on 67,099 square metres of land in Ahmedabad. There are similar allegations pertaining to his ashrams in Madhya Pradesh, Chhattisgarh and Rajasthan.

When people took to the streets following the gang-rape of a paramedical student in Delhi in December 2012, Asaram blamed the rape victim saying that the victim should have addressed her rapists as bhaiyya and requested them to leave her.

His follower Rahul Pachouri (24) was found dead under mysterious circumstances at the Jabalpur ashram in Febrauary 2013. Asaram was arrested in August for allegedly raping a minor at his Jodhpur ashram.