Despite an increased interest from the global change and resilience community, there is limited knowledge about the features and outcomes of polycentric governance. Moreover, there are few examples from the literature explaining transitions from lower to higher degrees of polycentric order. This seriously limits the explanatory power and application potential of the theory. The present study addresses this gap by investigating the global governance of nitrogen (N) and phosphorous (P) cycles. Those biophysical flows are two of the identified Earth-system processes in the “planetary boundaries” framework. This study explores governance challenges associated to these processes by analysing present institutional structures and actor collaborations. This is done by studying the network structures among all relevant multilateral agreements, EU (-level) Directives, and agreements on trade, combined with a more in-depth analysis of one global partnership initiative as a means to assess a possible emerging structure of polycentric order. The present study provides insights into how the current governance regimes in place for regulating the issues related to N and P flows look like, as well as issues and synergies of having a global partnership in place. The study suggests a global structure of polycentricity, which has the possibility to evolve into a better “match” with the dynamics of those biophysical flows through a larger governance context.