This article focuses on decision making for innovation management during product design. As such, it requires a holistic approach that determines the elements necessary for decision-making in knowledge-based organizations. The first part of this chapter explores the importance of the decision-making process, its role in organizational growth and development of strategies, as well as the high complexity that these processes have acquired over time in global and turbulent markets. Then, the decision-making process is detailed, recounting the elements that form it and the impact it has on organizations. Innovation and its classifications are later described, as well as its importance to modern economies. The importance of design, management and product development is also described. Case studies of companies operating in the Information Technology sector in Baja California, Mexico, are used to contextualize the research and demonstrate its validity for use during the development of new software products. Finally, the chapter concludes by exploring the relevance of this study, from a complex approach, using computational methodologies that increase the feasibility of carrying out decision-making with greater sustenance and expectation of success.