If innovation is the engine of economies, the partnerships in the Triple Helix model of innovation are the fuel that makes this engine work. Although each member of this model has its defined role, the present study sought to gain a new perspective on these partnerships, including the role of governments. Based on interviews with representatives of universities, companies, and governments in two countries (i.e., Portugal and Spain), this research focused on how innovation partnerships are formed as well as what obstacles to cooperation can arise. The results show that governments can play the role not only of a financier and legislator but also of a direct participant in innovation by entering into partnerships with the other Triple Helix actors. In addition, this study revealed that, irrespective of which partners and needs are in question, these networks operate mostly with public funds.