He has won several international awards such as the award for Best Picture at the Singapore International Film Festival, the Independent Film Festival of Brussels and Gawad Urian in 2002 and Netpac Jury Prize and Best Acting Ensemble (2001 Cinemanila International Film Festival) for his film Batang West Side (including Best Director, Best Screenplay, Best Actor, Best Supporting Actor, Best Cinematography, Best Production Design, Best Music, Best Sound at the Urian), in Gawad Urian in 2005 for the film Ebolusyon ng Isang Pamilyang Pilipino (Evolution of a Filipino Family), and Special Jury Prize at the Fribourg International Film Festival in 2006 for Heremias, Book One.
His films often tackle the issues regarding the current social and political state of the Philippines. His film Kagadanan sa Banwaan ning mga Engkanto (Death in the Land of Encantos), the Closing Film of the orizzonti section of the Venice Film Festival 2007, was awarded with a Golden Lion Special Mention. Death in the Land of Encantos was also in competition at the Artistic Innovation Award (Visions) of the Toronto International Film Festival 2007. He received several awards at the Palanca Memorial Awards for Literature. His film Melancholia won the Orizzonti Grand Prize at the 65th Venice International Film Festival in 2008. In January 2011 he joined the board of Directors for Cine Foundation International.
He is a recipient of the Guggenheim Fellowship in 2010, the Prince Claus Award of The Netherlands in 2014 and The Radcliffe Fellowship of Harvard University, 2016-2017.
He went back in 2011 at the Venice International Film Festival for his film Siglo ng Pagluluwal (Century of Birthing) and which earned the Grand Jury Prize at the 13th Cinemanila International Film Festival. The following year, his film Florentina Hubaldo, CTE won Best Asian Film at the Jeonju International Film Festival and gained the On-Screen Award at the Images Festival.
His 2013 film Norte, the End of History was screened in the Un Certain Regard section of 2013 Cannes Film Festival. He received the Golden Leopard at the 2014 Locarno International Film Festival for From What Is Before. At the 2016 Berlin International Film Festival, his film A Lullaby to the Sorrowful Mystery was awarded the Silver Bear Alfred Bauer Prize. He also received the Golden Lion at the 73rd Venice International Film Festival for The Woman Who Left.
