Four of their five most searched destinations this summer are in the region, with Bali topping the list.
It was followed by Singapore and Bangkok, Agoda reported based on its search data for May and June.
Dubai and Kuala Lumpur completed the top five.
Krishna Rathi, country director for Agoda for India, Sri Lanka and the Maldives, said the allure of Southeast Asia continues to captivate Indian travelers as they seek out new experiences and leisure opportunities.
"The diversity of destinations like Bali, with its serene beaches and rich traditions, along with the urban excitement of cities like Singapore and Bangkok, serves a broad spectrum of travel preferences.
"Furthermore, the many searches for Dubai and Kuala Lumpur show an inclination towards combining shopping, entertainment and cultural engagement."
Thailand and Malaysia have waived visas for Indians.
Other Southeast Asian countries such as Indonesia, Singapore and Vietnam are also considering visa-free entry for them.