Purpose The purpose of this paper is to test the mediating role of three types of innovation (product, process, and organizational) in the relationship between manufacturing flexibility and performance. Design/methodology/approach - Building on the resource-based view, the paper examines the indirect effects of manufacturing flexibility on organizational performance considering product, process, and organizational innovation as mediating variables. A sample of 159 Spanish firms is taken to test the proposed theoretical model through structural equations modeling using the partial least squares approach. Findings - The effect on organizational performance of adopting a flexible productive system is mediated by incorporating product, process, and organizational innovation. This paper calls for caution in defending flexible manufacturing systems as universally efficient solutions, and argues that their productivity is linked to the complementary introduction of organizational and technological innovations. Practical implications - Firms that pursue manufacturing flexibility should develop innovation capabilities to obtain an improvement in organizational performance. Therefore, managers should bear in mind that the mere fact of adopting a flexible manufacturing system will not guarantee improvements in firm performance. If manufacturing flexibility is to help improve company performance, managers should use this flexibility to generate organizational capabilities based on product, process, and organizational innovations, since these are capabilities that can create competitive advantages. Originality/value - Operations management literature has not reached a consensus about the effect of manufacturing flexibility on organizational performance. This paper helps both academics and managers to gain a better understanding of this question by considering the mediating effect of three types of innovation (product, process, and organizational) in this relationship.