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Clear-cutting alters natural ecosystem processes by reducing landscape heterogeneity. It is the dominant harvesting technique across the boreal zone, yet understanding of how environmental heterogeneity and beta diversity are structured in forest ecosystems and post-clear cut is lacking. We use ground-dwelling arthropods as models to determine how natural succession (progression from deciduous to mixed to coniferous cover types) and clear-cutting change boreal forests, exploring the role of environmental heterogeneity in shaping beta diversity across multiple spatial scales (between-cover types and between-stands of the same cover type (1600 to 8500 m), between-plots (100 to 400 m) and within-plots (20 to 40 m)). We characterise environmental heterogeneity as variability in combined structural, vegetational and soil parameters, and beta diversity, as variability in assemblage composition. Clear-cutting homogenised forest environments across all spatial scales, reducing total environmental heterogeneity by 35%. Arthropod beta diversity reflected these changes at larger scales suggesting that environmental heterogeneity is useful in explaining beta diversity both between-cover types and between-stands of the same cover type. However, at smaller scales, within- and between-plots spider beta diversity reflected the lower environmental heterogeneity in regenerating stands, whereas staphylinid and carabids assemblages were not homogenised 12 years post-harvest. Differences in environmental heterogeneity and staphylinid beta diversity between cover types were also important at small scales. In regenerating stands, we detected a subtle yet notable effect of pre-felling cover type on environmental heterogeneity and arthropods, where pre-felling cover type accounted for a significant amount of variance in beta diversity, indicating that biological legacies (e.g. soil pH reflecting pre-harvest conditions) may have a role in driving beta diversity even 12 years post-harvest. This study highlights the importance of understanding site history when predicting impacts of change in forest ecosystems. Further, to understand drivers of beta diversity we must identify biological legacies shaping community structure., Competing Interests: We have read the journal's policy and the authors of this manuscript have the following competing interests: the data collection took place on the EMEND experimental site, which receives some funding and support from two companies with commercial interest: Daishowa-Marubeni International Ltd. and Canadian Forest Products Ltd. This does not alter our adherence to PLOS ONE policies on sharing data and materials.