Most companies today experience a situation in which they are part of a complex business ecosystem of stakeholders that influence business outcomes. Especially for companies transitioning from selling products to becoming systems, solutions and services providers, this is causing a significant shift in their business strategies and relationships. Instead of focusing on internal processes, companies need to strategically position themselves in a dynamic network of actors to accelerate synergies and value co-creation. However, while this shift in business strategy is inevitable, it is not without challenges. An understanding for how to align internal, as well as external processes is critical, as well as a careful assessment on how to establish strategic partnerships in a dynamic network of interests. Based on on-going research, this paper outlines the emerging challenges that most software development companies face when adopting an ecosystem-driven approach, and the different mitigation strategies to manage these.