The research substantiates the need and relevance of introducing science-based methods into the practice of managing cash flows of the innovative industry in the context of maintaining environmental safety and implementing a strategy for greening production. The authors propose a method for managing an organization’s free cash flow based on constructing a matrix that includes a discrete set of outcomes and alternatives, as well as finding optimal solutions for the elements of the matrix using various decision-making criteria under conditions of uncertainty and the risk of negative impacts on the environment. The authors provide the characteristics of the application of these criteria in the practice of managing cash flows of the innovative industry. Moreover, the authors provide some recommendations for selecting the most suitable criteria to optimize the formation of an organization’s free cash flow under conditions of uncertainty and potential environmental risks. Moreover, the authors provide a practical example of implementing this method in an innovative metallurgical company that is adopting a green production strategy. This example includes an interpretation of the calculated results.