Obama told US Spanish language network Univision that the concert, which is expected to draw around half a million Cubans, could help improve ties with Cuba.
Obama's Secretary of State Hillary Clinton had met the Colombian singer before he left for Cuba, with both drawing criticism from Miami's Cuban exile community for a performance they say will legitimize the island's communist regime.
"My understanding is that he's a terrific musician. He puts on a very good concert," Obama told the station as part of a five-channel media blitz to sell his struggling efforts to reform US health care.
"I certainly don't think it hurts US-Cuban relations, these kinds of cultural exchanges," he added.
But he warned there was a limit to what cultural exchanges could achieve.
"I wouldn't overstate the degree that it helps," Obama said.
"What I'd really like to see is Cuba starting to show that it wants to move away from some of the anti-democratic practices of the past."
Tensions surrounding the "Peace without Borders" concert at Havana's Revolution Square even led to a death threat against Juanes, but ahead of the event the singer remained undeterred in dreaming the huge concert could usher in a message of unity.
"We are excited to connect with the audience in Cuba -- saying that we are here, that they are not alone, and that we hope over time things can change and the Cuban family can be one," the 37-year-old Grammy winner said Saturday.
"What better language than music... for that wake-up call," said Juanes, who now lives in Miami.
Juanes maintains that the event -- in the famous plaza that held countless rallies for former Cuban leader and revolutionary Fidel Castro -- "has nothing to do" with politics.
The show is the second event under the "Paz sin Fronteras" banner, after a 2008 Juanes show promoting peace on the border between Colombia and Venezuela.
The concert, headlined by Juanes -- most famous for his hit song "La Camisa Negra" -- will also feature some of Latin America's brightest music stars, including Olga Tanon, Danny Rivera, Silvio Rodriguez and the Orishas.