Indonesia's President Joko Widodo met with Obama at the presidential palace on the outskirts of Jakarta, with Obama delighting local media by greeting Widodo with "apa kabar" -- how are you in Indonesian.
The former first family arrived a week ago on the resort island of Bali and then visited the historic Yogyakarta city in central Java before coming to the capital.
President Widodo took Obama to a cafe in the botanical garden next to the palace, where he sampled traditional snacks and ate a bowl of meatball soup.
Obama spent four years in Indonesia in the late 1960s in the then-sleepy capital Jakarta after his mother married an Indonesian man, following the end of her marriage to his Kenyan father.
Many Indonesians feel a strong bond with Obama because of his early exposure to Indonesian culture, and a two-metre (six-foot) bronze statue has been placed in his former school.
The statue of "Little Barry", as Obama was known to his Indonesian school friends, depicts a young Obama dressed in shorts and a T-shirt with a butterfly perched on his hand.
Obama is travelling with his wife and their two teenage daughters.
Prior to Jakarta, they toured a Hindu temple wearing traditional sarongs, walked through terraced rice paddy fields and white water rafted in Bali.
They also visited ancient Buddhist and Hindu temples on Yogyakarta.
Obama is expected to give a speech about pluralism and tolerance at an Indonesian diaspora convention on Saturday before wrapping up his tropical holiday in the world's most populous Muslim-majority country.
Former US President Barack Obama, left, and Indonesian President Joko Widodo ride on a golf cart during their meeting in Jakarta. Source: AAP
