With reference to cohesion policy, multi-level governance (MLG) is the policy-making architecture that implements the subsidiarity principle, which aims for direct involvement bringing government closer to the citizen. In parallel, the partnership principle (PP) has been introduced to guarantee the participation of social and economic actors in both decision making and implementation processes in order to better understand and respond to territorial needs. A review of existing literature identifies opposing views on the benefit of this complex architecture. This paper investigates potentially conflicting effects of MLG and the PP on political accountability, for example by blurring responsibilities and corrupting stakeholder engagements. The Italian case is used to test this hypothesis and identify bottlenecks. Initial findings suggest that the empowerment of new actors by means of MLG has had the effect of disclosing political influence from several players in the decision-making arena, therefore obscuring the accountability of the different tiers involved both vertically and horizontally. This is because actors in the governance chain might tend to shift blame of policy failure towards higher or lower governmental levels. Additionally, the engagement of stakeholders may reduce the efficiency of implementation processes both through a lack of inclusiveness in the decision and policymaking style or through a lack of competences within civil society in interpreting local needs in relation to EU cohesion policy goals. This article concludes by outlining possible solutions for cohesion policy practice to minimize the negative consequences of a multi-tier/multi-actor system.