Purpose The purpose of this paper is to determine the effect of the co-alignment of structural variables on innovation, wherein Bogotá-based SMEs, belonging to the industrial, commercial and services sectors, were used as samples. Design/methodology/approach The study was conducted using a causal inference methodology and through the application of a structural equation model. Findings The results indicate that organizational structure has an influence on innovation, although this is true only for some variables and only when the analysis is performed separately. When performed under strategic co-alignment conditions, however, its influence becomes greater. Originality/value Organizational structure and innovation are determining factors of organizational performance. Although the strategic co-alignment theory has provided points of reference to understanding the phenomenon of organizational performance, there are still many gaps left to be filled. Additionally, it also requires empirical validation especially in relation to Colombian SMEs – and this is where this work makes a contribution.