Walking bare foot along the sea shore, he was seen picking up slippers from the sands normally given to guests staying at the five-star property.
In a series of tweets in keeping with his Swachh Bharat Abhiyaan, the Prime Minister also said "Plogging at a beach in Mamallapuram this morning. It lasted for over 30 minutes. Also handed over my 'collection' to Jeyaraj, who is a part of the hotel staff.
"Let us ensure our public places are clean and tidy. Let us also ensure we remain fit and healthy."
The video of Modi picking up waste from the beach was uploaded on his Twitter handle.
Modi also tweeted that he had a refreshing walk and also exercised along the scenic coast.
On Friday, Modi held the second informal summit with visiting Chinese President Xi Jinping in Mahabalipuram. The two leaders are set to hold more meetings on Saturday, where trade and business will be the main focus.