Demand for solving systemic problems has resulted in the need for new forms of innovation. Accordingly, the concept of innovation ecosystem has emerged. Ecosystems are intrinsically more fluid than networks, which set ups the need to understand and orchestrate the internal dynamics of innovation ecosystem in order to have successful innovation outcomes. The dynamics of ecosystems, however, is not well understood. In this paper the dynamics of innovation ecosystems has been studied by applying the methodology of system dynamics. The purpose of the study is to support the creation of innovation ecosystems and the orchestration of existing ecosystems so that they could be more successful. Key factors generating dynamics in innovation ecosystems were identified. They form the elements of the system dynamics model of innovation ecosystems. The causal loop structure between the model elements indicates how the key factors of dynamics influence the outcome of ecosystem.