- 2022/07 - National Book Development Board and Manila Critics' Circle 39th National Book Award of the Philippines, Best Novel in English "Tiempo Muerto: A Novel"
- 2022/04 - Writers' Union of the Philippines (Unyon ng mga Manunulat sa Pilipinas) Balagtas Award (Gawad Pambansang Alagad ng Sining) Gawad Balagtas for Literary Criticism and Fiction in English
- 2021/11 - Book Development Association of the Philippines Gintong Aklat Award for Fiction in English "Tiempo Muerto: A Novel"
- 2021/03 - Philippine Studies Group of Association of Asian Studies (USA) Grant Goodman Prize in Historical Studies Lifetime Achievement Award
- 2019/11 - Manila Critics Circle and National Book Development Board of the Philippines 38th National Book Award of the Philippines Best Book of Literary Criticism/Literary History, "Interpreting Rizal"
- 2018/10 - Manila Critics Circle and National Book Development Board of the Philippines 37th National Book Award, Philippines Best Book of Literary Criticism/Literary History, "Elites and Ilustrados in Philippine Culture"
- 2017/10 - Manila Critics Circle and National Book Development Board of the Philippines 36th National Book Award, Philippines Best Anthology (Bilingual), "Remembering/Rethinking EDSA"
- 2016/10 - Manila Critics Circle and National Book Development Board of the Philippines 35th National Book Award, Philippines Cirilo F. Bautista Prize for Best Book of Short Fiction in English, "Recuerdos de Patay and Other Stories"
- 2011/01 - Philippines Free Press Magazine Philippines Free Press Literary Award Grand Prize, Fiction Category, “Recuerdos de Patay”
- 2005/10 - Manila Critics Circle and Philippine National Commission for Culture and the Arts 2004 National Book Award, Philippines Literary Criticism, "On the Subject of the Nation: Filipino Writings from the Margins, 1981-2004"
- 2001/10 - Manila Critics Circle and Philippine National Commission for Culture and the Arts 2000 National Book Award, Philippines Criticism, "Necessary Fictions: Philippine Literature and the Nation"
- 2001/10 - Manila Critics Circle and Philippine National Commission for Culture and the Arts 2000 National Book Award Anthology, "Intsik: An Anthology of Chinese Filipino Writing"
- 2000/12 - Book Development Association of the Philippines Gintong Aklat (Golden Book) Award Literature,Carlos Bulosan’s "All the Conspirators" (edited by Caroline Hau)