When aiming at studying the interconnectedness of administrative systems and in particular the integration of domestic governance systems and the institutions of the European Union at least two variables are important to address: (i) the intensity and frequency of cross-level interaction and participation amongst the members of these systems, and (ii) the principles of organization being uppermost at both levels of governance. This article argues that in order to measure administrative integration, particular emphasis should be attached to the way these variables impact upon the organization members individually. Put more precisely, I argue that studies of administrative integration should analyse how and why cross-level participation foster changes in the identities, role conceptions and modes of acting amongst the organization members of these systems of governance. When aiming at accounting for these processes, this article stresses the effects of primary and secondary institutional affiliations, and the dynamics stemming from the degree of compatibility between the two. Processes of administrative integration are fuelled by high degree of cross-level compatibility in organizational structures, and secondly, by the sheer intensity and length of cross-level participation. Thirdly, I argue that administrative systems being organized according to the principle of purpose foster administrative integration more strongly than administrative systems organized according to the principles of area. Hence, I argue that the EU Commission is more likely to foster administrative integration across levels of governance than the Council of Ministers.