The large environmental impacts associated with agro-industrial development in Indonesia are both striking and increasingly important, especially with increased demand for biofuels and the rapid extension of oil palm plantations. Recently, Indonesia has also seen a series of transformations in the regulatory regime for pollution control with decentralization and a shift towards new environmental policy instruments. This article considers the effectiveness of these new approaches, including the widely influential International Organization for Standardizations (ISO) 14001 series for environmental management systems and the Roundtable on Sustainable Palm Oil (RSPO) certification system. Despite the turn towards these new governance approaches, the underlying problems that have undermined bureaucratic regulation in the past continue to haunt attempts to make the sector more sustainable. Efforts to mitigate the increasingly large-scale pollution associated with agro-industrial development will need to be better crafted and combined to suit the characteristics of the industry concerned and to address the wider socio-economic and political realities within which problems are embedded and where any policy tool must be applied.