The Basque border area represents a test case for the transformations of territorial governance and the structuring of alternative economic spaces. This paper is based on the qualitative analysis of 26 cross-border projects related to the social and solidarity-based economy (SSE), in distinct sectors (Basque language and culture, agroecology, fishing, media, women entrepreneurship, social integration and social services). The first hypothesis relates to the historical sequences of this cooperation from below that anticipated the formal institutionalization of a cross-border cooperation policy. Civil society actors, nevertheless, were prompt to seize the new policy instruments of cross-border cooperation that emerged in the 1990s. The 2008 economic crisis generated new forms of cross-border governance: the initial enthusiasm for the Europe of the regions decreased, and hybrid interactions between SSE, policy makers and private businesses increased. Our second hypothesis relates to the asymmetries that the actors have to overcome in order to build effective cross-border governance networks: institutional asymmetries between different levels of decentralization, political asymmetries between functional and political perceptions of cross-border cooperation; organizational asymmetries between different SSEs; market asymmetries finally, with the risk of a “back-to-back” and instrumental cooperation only motivated by the access to EU-based or bilateral funding opportunities.