How does intra-institutional conflict within the Commission play out vis-à-vis the Council? What are the conceptual consequences of modelling the Commission as collective agent? And how does preference heterogeneity among its constituent services affect its ability to influence European policy? In addressing these three interrelated questions we adopt a Principal–Agent (PA) perspective. Previous contributions frequently focused on the Council qua collective principal and found a negative impact of preference heterogeneity on its ability to rein in the Commission. By contrast, the Commission-as-agent has often been conceptualized as a unitary actor despite its increasing complexity. Recently the PA literature abandoned this simplification and started investigating how collective agent features may play out in a setting of political delegation. This paper adds to this recent theoretical development by investigating the effect of intra-Commission dynamics with regard to the EU’s trade policy, which is among the policy areas most heavily studied from a PA perspective. After presenting the theoretical state of the art and defining key concepts, the empirical analysis adopts a longitudinal research design to analyze four trade agreements between 1970 and 2002 with varying degrees of conflict among Commission services. The earlier cases are a useful complement to contemporaneous agreements by providing deeper insight through archival sources. We conclude that conflict within the Commission is more quickly resolved than in the Council due to the more hierarchical mode of preference aggregation. The unitary actor assumption may thus be more appropriate than may appear from its complexity. In fact, the Commission may benefit from preference heterogeneity by charging services to follow parts of the dossier that are fiercely contested by certain Member States, thus reducing the likelihood of involuntary defection at the end.