The need to feed an increasing world population and to respond to the effects of climate change creates unprecedented challenges for bio-based production systems. Many of these systems have been designed to maximize productivity and efficiency under standard conditions, increasing their vulnerability to changes in their surrounding natural, technological and social systems. Reviewing the recent literature and reflecting on current research, we find that dominant attempts to increase production focus on maximizing control, while insufficient attention has been paid to system resilience, adaptability and transformability. These three core aspects of resilience thinking aim to reduce system vulnerability. We therefore argue for stronger adoption of resilience thinking into research on bio-based production systems. We show how applying resilience thinking helps to address both the production and the vulnerability challenges through interdisciplinary collaboration and cross-fertilization.