In this paper we investigate, using a multi-level perspective, how innovations can change the relation between multiple socio-technical systems. We analyze two Dutch cases: the use of biomass in the waste and the electricity regime, and CHP in relation to the natural gas and electricity regime to explore boundary crossing dynamics. We conclude that these dynamics radically changed the way the regimes relate from almost no relation to a much more symbiotic and even integrative relation. We also find a pattern where the presence of more than one regime seems to offer extra opportunities during the early phase, but creates barriers further along the innovation path. Additionally, we introduce a typology for investigating and understanding boundary crossing innovations. Policy consequences of border crossing dynamics are still far from developed; connecting disconnected policy arenas might be the most important challenge.