This chapter explores the central question, for the organization agrifood chains, of alignment between governance of quality and Quality Management Systems (QMSs) when these chains are rooted in different components of territorial dimensions (“territory-based agrifood chains”). Based on a literature review, we start with the core argument of alignment. Studies on territory-based agrifood chains are rare; moreover, the alignment principle does consider the territorial dimension per se. Thus, the issue explored in this chapter is to identify specific characteristics of these territorial dimensions, their complexity on the ground, and the characteristics of products necessary to fulfill the alignment principle. To do so, we developed a two-step approach. First, following theoretical studies on the alignment principle and its application to agrifood chains, we defined an analytical framework based upon an original dimensionalization of connections between territories and QMS and between territories and governance of quality. It allowed us to extend the concept of alignment by considering simultaneously, in concrete case studies, the interplay between QMS and governance of quality when chain actors are embedded at multiple territorial levels. We conclude by emphasizing the importance of knowledge about the alignment principle when one wants to implement quality in territory-based agrifood chains successfully.