For many countries, the pursuit of innovation is not just a matter of growth but also one of sovereignty. This chapter explores how the ability to generate, control and apply knowledge becomes a question of independence in a world shaped by global value chains, digital platforms and shifting geopolitics. It traces how reliance on foreign technology and multinational enterprises can leave economies vulnerable, dependent on decisions made elsewhere and unable to chart their own development paths. At the same time, it examines how building domestic capabilities through investment in research, strong institutions and inclusive policies can create the foundations for greater autonomy. Yet sovereignty in innovation is never absolute; it requires balancing openness with resilience, integration with self-reliance. The chapter argues that the challenge for emerging innovation systems is not to isolate themselves, but to secure enough strategic capacity to ensure that innovation serves their societies, rather than leaving them perpetually at the margins.