An organization’s capability to build, handle and exploit relationships and learn from these relations, defined here as relational capabilities, is increasingly important in a networked economy and in innovation activities. The paper introduces a framework that helps understand and analyse the relational capabilities of various organizations engaged in innovation activities. Based on theoretical discussion and empirical analysis the paper argues that the literature on organizational level capabilities and relational capabilities would benefit from deeper integration with the systems of innovation perspective. The empirical findings from three Finnish regions indicate that relational capabilities become particularly relevant in research–business–government cooperation contributing to innovation in the field of bioeconomy. Relational capabilities embedded in an organization’s capability configurations can boost the efficient use of that organization’s resources, bring greater flexibility, a chance to create value in networks and support renewal and innovation. Missing or underdeveloped relational capabilities may also hinder an organization’s ability to tap into the economic opportunities that arise leading to failures at the regional and system level thus hampering the transition towards a bioeconomy.