Little is known about the effects of the inter-institutional linkages created through the establishment of the codecision procedure on decision-making in the Council of the European Union. After a review of the existing literature and theories on this topic, we examine to what extent the codecision procedure leads to more involvement of ministers in Council decision-making and to a more powerful position of the Presidency in the internal negotiation process of the Council. The results show that the initially positive effect of codecision on the politicization of Council decision-making has been offset in recent years by a growing lack of transparency in inter-institutional proceedings caused by the use of informal trialogue negotiations to conclude the procedure early. However, our study also suggests that the country holding the Presidency does not occupy a more privileged position in the Council’s internal co-operation network as a result of these developments. Thus, with respect to the Council, informal inter-institutional negotiation practices seem to decrease the transparency of the decision-making process and the accountability of the actors involved, but they may not have as adverse an effect on who gets what in terms of policy as previously thought.