Biofuels development has assumed an important role in integrating Indigenous peoples and other marginalized populations in the production of biofuels for global consumption. By combining the theories of commoditization and the environmental sociology of networks and flows, the author analyzed emerging trends and possible changes in institutions and behaviors brought about by the introduction of biofuels as a development option on ancestral lands. Using the Indonesian oil palm and the Philippine Jatropha experiences, the author argues that although there are efforts to integrate smallholder systems to the global integrated biofuels network, the effects of commoditization continue to undermine the more sustainable, less commoditized agricultural practices of Indigenous peoples. Indigenous peoples and their traditional agricultural practices are at risk of being either phased out from or eventually transformed by the global integrated biofuels network to accommodate.