This article contributes to the understanding of inter‐agency coordination among international organizations, conceived as international public administrations (IPAs). We adopt a practice‐based approach to study the dilemmas of coordination across levels of government in the empirical setting of United Nations agencies involved in field‐level development activities. Based on elite interviews in both pilot countries and agency headquarters, complemented by extensive archival analysis, we track the emergence of a specific type of coordination dilemma that has been understudied, that is, the dilemma of inter‐ and intra‐agency coordination. We identify two sets of coordinating practices that aided in balancing the dilemma, that is, ‘systemic thinking’ and ‘jointly mobilizing resources and consensus’, and we discuss the organizational factors mediating the perception of each set of practices.