By Agence France-Presse
Bun Cha Huong Lien restaurant in the Vietnamese capital's leafy Old Quarter soared to fame after the 2016 sit-down between Obama and Bourdain for his CNN show.
The pair shared a simple meal of pork noodles and fried spring rolls -- each dish worth around $3 -- and photos of the casual dinner quickly went viral.
Bourdain died by suicide while in France filming an episode of his Emmy-winning CNN food and travel program "Parts Unknown", the network said Friday. He was 61.
"I was surprised and sad when I heard about (Bourdain's) death," Nguyen Thi Nga, co-owner of Bun Cha Huong Lien restaurant told AFP.
"(Bourdain) was a nice, friendly and folksy person... He praised our bun cha dish and its fish-sauce broth. He loved Vietnamese food," Nga said.
Obama posted a tribute on Twitter to Bourdain on Friday, sharing a picture of the pair drinking beer during the meal which took place during his state visit to Hanoi.
Bourdain came to Vietnam several times throughout his life, making several TV programmes about his fascination with the country's food.
Inside the restaurant, as hungry customers poured in for lunch on Saturday, diners gave extra attention to the glass box in which the table and chairs used by Bourdain and Obama are preserved.
"I came here to share the grief of the loss of such a talented chef... he was a such a special person because he had such a great passion for Vietnamese food," customer Nguyen Quan told AFP.