Flores' work articulates how culture is represented, identified, produced, consumed and regulated within Latino diasporic communities in more recent times.
Theory of diaspora and transnational communities
In his book The Diaspora Strikes Back: Caribeño Tales of Learning and Turning, Flores distinguishes between “new diasporas” and those of earlier time periods by noting the difference in “the intensity and reciprocity of the ties between emigrant or exiled populations and their countries of origin”. Flores regularly uses the analogy of seeds being spread and growing where they land to describe the Latino diasporic experience. Flores describes the culture formed in the communities where they reside as dynamic and continuously changing due to the exchange of cultural remittances. He focuses specifically on the transculturation that occurs as groups move from their homeland to the U.S. and back.
Afro-Latino culture
Much of Flores' work on the Afro-Latino culture has focused on its progression in the United States. In The Afro-Latino Reader, he analyzes the way in which Afro-Latinos are racially categorized according to Eurocentered colonial standards and how this categorization changes according to location.
2000: From Bomba to Hip-Hop: Puerto Rican Culture and Latino Identity - In this book, Flores describes and celebrates the unique role of Puerto Rican culture in the music, literature and other pop culture in their more recent history in the United States.
2004: Cortijo's Wake - Juan Flores translated this piece by Edgardo Rodríguez Juliá, describing the funeral of Puerto Rican musician Rafael Cortijo.
2007: Companion to Latino Studies - A collection of 40 original essays written by leading scholars in the field, dedicated to exploring the question of Latino/Latina identity.
2009: The Diaspora Strikes Back: Caribeño Tales of Learning and Turning - In this book, Flores examines the “new” diasporic process and the effects that this transnational movement has on the home country.
2010: Bugalú y otros guisos: ensayos sobre culturas latinas en Estados Unidos - Describes Latino culture in the United States.
2011: The Afro-Latino Reader - Includes a selection of more than sixty scholarly essays, short stories, newspaper and magazine articles, memoirs, interviews and poetry that discuss the unique social and ethnic categorical position of Latinos of African descent in the United States and throughout the Americas.
His current projects include: Companion to Latino Studies.