A range of studies from Earth system scientists argue that human activities drives multiple, interacting effects that cascade through the Earth system. Recent contributions state and quantify nine, interacting «planetary boundaries» with possible threshold effects. This article provides an overview of the Earth system governance challenges that follow from this notion of multiple, interacting and possibly non-linear «planetary boundaries». Here we discuss four interrelated global governance challenges, as well as some possible ways to address them in future research. The four identified challenges are related to 1) the interplay between Earth system science and global policies; 2) the capacity of international institutions to deal with individual planetary boundaries, as well as interactions between them; 3) the role of international organizations in dealing with planetary boundaries interactions; and 4) the role of Earth system governance in framing social-ecological innovations.