Bourdain arrived in the capital late Thursday, according to a source at the Ninoy Aquino International Airport.
Another source said he is in the country to film episode for his television show, Parts Unknown, which features food and culture of diverse peoples around the world.
The Philippine Daily Inquirer carried a photo of Bourdain eating in a restaurant, while local television reporter Jam Sisante tweeted photo of the chef posing with fans, also inside a restaurant.
"Word on the street is Anthony Bourdain is here in Manila already. Where is he eating?! I wanna know!" Christel Boncan tweeted.
"Welcome back to Manila Anthony Bourdain! Hope you can drop by Mercato Centrale to support pinoy (Filipino) startup," the Mercato Centrale restaurant tweeted.
Another fan, Inna Aldeguer, pleaded for Bourdain to let her be the one to show him around Manila.
Bourdain first came to the Philippines in 2008 for his show, No Reservation, in which he traveled to Manila, and the provinces of Pampanga and Cebu to sample local cuisine.