The objective of this article is to assess the implications of iterative learning in organizations that establish and lead modular networks of innovation that create complex systems. This article focuses on the analysis of the dynamic phenomena that occur when a system performs its functions through subsystem interactions in its operational environment. Herein, it is argued that learning by using is a distinct epistemological class, which is practice-oriented, to the extent that it requires the reflective confrontation of previous stock of knowledge and that derived from praxis, which is concrete, dynamic and relational. In these cases, subsystems design and interfaces refinement cannot be deterministically understood as a set of problem resolutions that will naturally occur. Instead, these dynamic phenomena emergent properties can generate causal ambiguity situation, which arises from functionalities coupling. By taking a resource-based view of the firm, this article discusses the importance of learning by using in the systems integration capabilities building. It proposes a model that considers the domains of knowledge, organization, and product within a project-based organization framework.