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Accurately representing within-canopy microclimatic processes remains a major challenge for vegetation and climate models. Most Land Surface Models (LSMs) and Earth System Models (ESMs) rely on simplified canopy representations that fail to resolve the effects of vertical gradients of temperature and vapor pressure deficit (VPD), despite their critical role in regulating plant physiology, forest dynamics, and biosphere–atmosphere exchanges. While multilayer canopy models improve the representation of these gradients, they often lack the structural and demographic realism needed to link microclimate to long-term forest dynamics.Here, we use the individual-based forest model TROLL to compare simulations that include or neglect within-canopy microclimatic buffering, and to assess its influence on physiological fluxes, forest structure, and long-term carbon storage. TROLL explicitly represents individual tree growth, mortality, three-dimensional structure, and competitive interactions, allowing environmental conditions to vary vertically and to be experienced by trees according to their position within the canopy. To disentangle short-term and long-term effects, we decompose ecosystem fluxes over the last decade of the simulations, isolating physiological and structural responses from emergent centennial-scale patterns.Preliminary analyses suggest that microclimatic buffering affects gross primary productivity (GPP) and transpiration in contrasting ways. These metrics do not always respond in the same direction, with distinct, and sometimes decoupled, responses across vegetation layers, reflecting differences in exposure, hydraulic constraints, and trait-mediated regulation. Aboveground biomass also shows non-intuitive responses to microclimatic buffering, highlighting the limits of interpreting forest functioning from fluxes alone.Over centennial timescales, simulations including microclimatic buffering lead to forests characterized by lower atmospheric demand, reduced hydraulic stress, and ultimately higher aboveground biomass, despite lower photosynthetic fluxes. These long-term differences emerge from the cumulative effects of short-term physiological regulation and size-dependent mortality, which selectively favors individuals less exposed to thermal and hydric stress.By explicitly linking microclimatic buffering, ecosystem fluxes, and demographic processes, this study provides a mechanistic explanation for how within-canopy microclimatic heterogeneity can enhance forest carbon storage while dampening ecosystem-level fluxes. Our results highlight the importance of representing microclimatic buffering and individual-level processes to improve predictions of forest resilience under ongoing climate warming.