Aim: Polar and alpine plants live at the edge of their physiological limits. Thus, relatively small changes in climate can have disproportionate effects on biological and ecological processes. Antarctic mosses display highly variable micro-topography (canopy architecture) over centimetre scales that correspond with spatial patterns in moss health. We aimed to assess the influence of centimetre-scale micro-topography on biologically relevant canopy microclimates across Antarctic moss beds. Location: Trans-Antarctic. Time Period: 2018–2023. Major Taxa Studied: Moss communities (bryophytes). Methods: Spatially explicit microclimate data were measured (canopy temperature and water content) at different micro-topographic positions (micro-ridges and valleys, and various micro-slopes and aspects) within 1 m2 plots of continuous moss cover in Maritime and East Antarctica. Solar radiation was modelled at 1 cm2 resolution. Results: (1) Moss canopies varied by up to 2.24°C in mean and 15°C in maximum temperature within plots, with centimetre-scale micro-topography consistently shaping microclimate conditions. (2) Micro-topographic position, seasonal solar dynamics and processes such as radiative trapping jointly influence the spatial structure of moss temperatures over centimetre scales. (3) East Antarctic mosses show a greater ability to warm above ambient air temperature compared to Maritime Antarctic mosses and may be especially at risk of exceeding upper temperature thresholds. Main Conclusions: This study considers the effect of centimetre-scale moss micro-topography on moss canopy microclimates and more broadly offers novel insights into the spatial structure and variation of ground-level climate over scales typically overlooked by in situ measurements. We discuss centimetre-scale microclimate variation in terms of moss physiology and observed declines in the health of East Antarctic mosses which visibly map to the micro-topography. These findings are especially relevant for regions across the globe with short-stature vegetation, like bio-crusts, and alpine and polar fellfields. Recognising climate variation at micro-topographic scales is crucial for understanding ecophysiology and plant–climate interactions.