Biodesign is an emerging field that brings together a wide range of practices, connecting fundamental research, applied sciences, and creative approaches. Within this spectrum, a tension exists between instrumental uses of biological processes and a growing sensibility that acknowledges the agency of living materials and organisms. This study proposes Reconciliation as a guiding concept for biodesign, understood not as a metaphorical gesture but as a concrete and plural perspective that promotes species coexistence and conservation. We contextualise Reconciliation through Restoration, Reciprocity, and Relationality as distinctive yet interconnected design and ecological principles that extend beyond normative human exchange, promoting multispecies coexistence. Through a mix of reflexive thematic synthesis and the analysis of selected case studies derived from the authors’ own projects, employed as a practice-based methodological inquiry and primary source of empirical and reflective insight, we explore how Reconciliation is enacted and experienced in practice. Finally, we propose a conceptual framework to address Reconciliation in biodesign, offering guiding concepts and key questions to discuss and support ecological flourishing in multispecies collaborations.