Innovation management and economic sustainability have become one of the business challenges to consolidate. given the above, the objective of the study is to determine the relationship between innovation and economic sustainability in small and medium-sized enterprises (SMEs) in Latin America. through an empirical study, 2660 SMEs were examined, 1729 small and 931 medium-sized, located in 13 Latin American countries. the data obtained by applying a survey were processed using a non-linear canonical correlation analysis (NLCCA). The findings identify functional and operational risks in SMEs that weaken innovative potential, in addition to technical-operational barriers—lack of knowledge and low investment that limit economic sustainability, whose importance transcends towards transformations of business models and effectiveness of resources that promote business sustainability. contributions are suggested for the management of public policies aimed at strengthening innovation and economic sustainability to project the emerging economies of Latin America.