The concepts of industrial symbiosis (IS) and bioeconomy (BE) both focus on ways to reduce dependence on non-renewable resources. However, these two frames of reference have rarely been considered as part of a joint strategy to achieve sustainability. Here, we describe how they inter-operate, in well documented IS case studies, to identify current synergy patterns of organic by-products, their limits, and promising pathways towards integrated initiatives that pursue the respective goals of each framework. We first evaluated the nature of synergies in current practices, and how they contribute to sustainability. Second, we focused on the role of agriculture in these symbioses, due to its fundamental role in circular bioeconomy. We used three main dimensions to analyze our case studies: IS emergence, governance of synergies, and actor serendipity. We identified three main patterns of organic matter use within IS, which we termed metabolic resources, metabolic biorefinery, and global biorefinery. Our observations suggest that synergies with agriculture are undervalued, by both internal and external practitioners. We conclude that while the combination of BE and IS can bolster sustainability, it requires a dedicated implementation strategy that has yet to be conceived.