Traditional research funding structures are increasingly misaligned with the distributed, digital, and collaborative nature of scientific work. Decentralized Science (DeSci) initiatives, using blockchain-based governance models such as decentralized autonomous organizations (DAOs) and tokenized ownership, propose experimental mechanisms to address these systemic bottlenecks. This research-in-progress adopts a critical realist case study approach to examine how DeSci DAOs reshape principal–agent relationships and governance structures within polycentric systems. Combining interviews, on-chain governance metrics, and archival analysis, we aim to uncover how decentralized architectures reconfigure incentives, participation, and decision-making. Grounded in Principal–Agent Theory and Polycentric Governance, the study seeks to advance understanding of the affordances and tensions inherent in digital governance mechanisms for new research funding approaches. By examining how distributed infrastructures reshape coordination, incentives, and participation in scientific collaboration, this work offers critical insights into the evolving dynamics of research governance in digitally mediated environments.