The developing bio-energy and bio-product based industries that are driving the new bioeconomy pose significant biosecurity risks around the potential of associated new crops to (a) escape the agricultural systems within which they are expected to generate value to invade and cause economic or environmental harm elsewhere, (b) attract new pests that reduce yields or the yields of other related food crops in the landscape and (c) contaminate field to end product production chains of food crops when the same crops are being used. We discuss how best to use science to risk assess and provide solutions to predict likelihood new crops could turn feral and how to avert any negative consequences from a policy/regulatory standpoint. We also discuss how best to use science and public'private investment to ensure that such crops are managed sustainably with respect to pests and diseases, and manage the pest-disease risks that new crops pose to existing agricultural systems in a landscape context. Following this we focus specifically on the future policy and science needs to more effectively address these biosecurity imperatives. Science-based processes for assessing new crops for potential environmental risks they may pose as invaders are now well established and increasingly being adopted internationally, but their adoption in the developing world needs assistance and their effectiveness will be driven by jurisdictional perceptions of such risks. Such risk assessments in new regions can also benefit from previous experiences with GM crops. The application of sustainable pest management strategies to new non-food cropping will require public'private R&D investment to ensure against such threats.This is needed to insure public investments, such as subsidies and incentives, in these new crops against pest induced crop failure. Finally we outline fourteen recommendations we agreed were important globally to progress these biosecurity issues in the new bioeconomy to prevent greater environmental harm and pest disruptions than are already being experienced in agro-forestry systems. These recommendations also consider how best to assist poorly resourced developing countries on these issues. The outputs of this paper aim to provide foci of engagement for scientists, policymakers and industry stakeholders to better coordinate future needs and required responses to these potential biosecurity issues in the new bioeconomy.