Originally named "Murugan Coffee Nilayam," the original Madurai branch only served coffee, snacks, and idlis.[2][3] In 1991, the new owner of the restaurant changed its name and significantly expanded the menu.[4] The first Chennai branch was subsequently established in 2003.
In 2019,the licence of its central kitchen based at Ambattur Industrial Estate was suspended due to unhygenic and adverse sanitary conditions.[5][6][7] Additionally, on a complaint filed by a customer, notice was issued by officials from the Chennai division of the Department of Food Safety and Drugs Administration to a Murugan Idli Shop outlet located at Parry’s Corner.