Biocrust communities promote soil surface roughness, a key functional characteristic for soil ecology. However, the spatial scales at which biocrust communities contribute to surface roughness are not well understood. To refine our understanding of the spatial dynamics between biocrust and soil surface roughness, we used mm-resolution terrestrial LiDAR to measure micro-topographic roughness at seven sub-meter, 3-dimensional kernels (spatial scales) for undisturbed and disturbed biocrusts within the cool Great Basin and the hot Chihuahuan Deserts of western North America. This multi-scalar approach applied within the different desert regions allowed us to explore two objectives: 1) assess the relative importance of climate and disturbance on biocrust roughness, and 2) evaluate how soil surface roughness evolves with biocrust recovery. For objective 1, we found that undisturbed cool desert biocrust was up to three times rougher than hot desert biocrust. Much of the difference in roughness between the two desert biocrust communities appeared to be from climate or other regional factors. However, positive correlations between roughness and biocrust indicators, including soil chlorophyll-a and the field-based Level of Development (LOD) index, suggested that differences in roughness at spatial scales ≤ 10 cm are directly related to biocrust development. Mechanical disturbance aimed at removing biocrust resulted in significant reductions in roughness and removed much of the observed differences in roughness between cool and hot desert soils. We evaluated biocrust recovery within the cool desert study area two years after mechanical disturbance and found that the disturbed soil increased in roughness up-to 300%. The increased surface roughness at spatial scales ≤ 10 cm were positively correlated with increased aggregate stability and indicators of biocrust reestablishment. We found that topographic change area was also an important contributor to roughness at all spatial scales, particularly at spatial scales ≥ 20 cm where it was the most important factor evaluated. These results provide insight into how biocrust interacts with other biophysical processes to influence soil surface roughness and how soil surfaces evolve at time scales relevant to soil restoration activities.