Identifying and assessing risk is one of the most important processes in managing complex systems and requires careful consideration. The need for an effective, efficient approach to risk management is considerably more important for defense industries, because they are exposed to risk in the early stages of development. This paper uses heterogeneity and homogeneity analysis between risk factors with Cochran’s Q test and multidimensional scaling in order to present the complexity of the risk factors relevant to defense systems of systems (SoSs), and it proposes a methodology for identifying, analyzing, and monitoring the risks that they face. Findings from an in-depth analysis of 46 classified defense SoSs shows a need to focus on three main risks faced by defense projects: insufficient human resources, changes in the original specifications, and lack of other (nonhuman) resources. The paper also presents some recommendations for minimizing risk factors in defense SoSs.