Climate change is reshaping ecosystem structure, functioning and biodiversity worldwide, yet the role of abiotic landscape heterogeneity in mediating ecosystem responses remains poorly understood. Geodiversity has recently emerged as a key factor for ecosystem resilience, potentially influencing biodiversity patterns, ecosystem functioning and the capacity of ecosystems to adapt to environmental changes. However, the extent to which interactions between geological and biological features affect ecosystem processes remains largely unexplored. To address this gap, we quantified CO₂ fluxes across contrasting geo-biological associations in the Folafótur Peninsula (Westfjords, north-western Iceland), including heathlands on volcanic bedrock, wetlands on sedimentary substrates and meadows on marine terraces. Two replicate plots were established within each association to evaluate differences in geodiversity, biodiversity and ecosystem carbon dynamics. We unveil that distinct geo-biological associations exhibited marked differences in gross primary productivity (GPP) and ecosystem respiration (ER), with variation among associations exceeding that observed among environmentally similar replicate plots. Notably, geo-biological associations explained a substantial proportion of carbon-flux variability beyond that accounted for by established environmental drivers such as temperature and irradiance. Although biodiversity and geodiversity metrics did not consistently covary, divergence metrics clearly distinguished the different associations, highlighting the importance of considering both biotic and abiotic dimensions of ecosystem heterogeneity. These findings suggest that geo-biological associations represent an overlooked source of variability in ecosystem carbon dynamics and may contribute to shaping ecosystem responses to climate change. Integrating geodiversity into biodiversity and ecosystem-function research could improve the identification of vulnerability and resilience hotspots, supporting conservation and land-management strategies aimed at enhancing ecosystem adaptation and maintaining climate-regulating ecosystem services under global change.