Transdisciplinary research (TDR) aims to co-produce knowledge to address the complex challenges of unsustainability. Despite progress in articulating principles for successful co-production, Indigenous researchers have pointed out ongoing power imbalances. These disparities, partly stemming from unacknowledged ontological-epistemological inequalities, often perpetuate hidden hierarchies between researchers and participants. At the core of these power imbalances is the dominance in academia of certain ways of knowing (e.g., categorical, experimental, noun-based, substantialist) over others (e.g., relational, experiential, verb-based, idealist). This bias is formalized and reinforced by academic institutions and cultures, passed down and internalized through education and professionalization. Inclusive TDR needs to break this self-reinforcing cycle, but this requires making inner room for multiple perspectives on reality and existence. To explore how inner work may foster ontological pluralism and inclusive TDR, we held a workshop drawing lessons from three case studies of TDR from Malaysia, Botswana, and Ecuador. Participants’ experiences were synthesized into a reflexive cycle of five inner shifts toward inclusive TDR. These shifts enhance the ability of researchers to engage with different ontologies beyond scientific materialism, and recognize their embeddedness in various kinds of relationships, extending their relational awareness to other beings, human and non-human, living and non-living. The proposed reflexive cycle seeks to cultivate capacities for co-production in TDR that are grounded in horizontally inclusive research practices that allow for more contextually relevant and impactful solutions to complex real-world problems.