This study develops a multilevel conceptual model of resource transformation in biogas-based industrial symbiosis (IS). It examines how residual flows such as digestate, carbon dioxide (CO₂), and heat become strategic resources through coordinated technological, organisational, and institutional processes. Using bibliometric science mapping of 228 peer-reviewed articles (1990–2024), combined with theory-driven interpretation, the study identifies dominant research patterns and underlying structural relationships in the field. The analysis reveals three cross-cutting mechanisms—resource conversion, coordination, and institutional stabilisation—that structure resource transformation across micro-, meso-, and macro-levels. The findings show a shift in the literature from technology- and efficiency-oriented perspectives toward systemic, multi-actor, and policy-embedded understandings of circular innovation. Building on this, the study develops a mechanism-based conceptual synthesis that explains how value emerges through the alignment of technological processes, inter-organisational networks, and institutional conditions. The study further illustrates how Natural-Resource-Based View (NRBV) concepts can be applied in a multilevel context, showing that VRIN (valuable, rare, imitable, non-substitutable) characteristics are not inherent properties of resources but emerge through coordinated processes across system levels. Finally, it proposes analytically derived propositions and guiding principles for practice that highlight the conditions under which IS systems may develop and scale. © 2026 The Authors.