Downed woody debris (DWD) creates heterogeneous microsites that are beneficial to enhancing biodiversity and that represent persistent nutrient and carbon pools. Windthrow events characteristic of northern deciduous forests naturally produce abundant DWD and canopy openings that enhance structural complexity, but group selection harvesting reduces DWD biomass despite promoting vertical structural complexity. We implemented a field experiment to test the response of the soil microbial community (SMC) to DWD addition in created gap openings to compare experimental windfall to group selection harvest. Our objective was to assess the variability among microbial functional groups within canopy openings versus at the stand scale with DWD addition four- and five-year posttreatment. This study builds on previous studies at the Flambeau Experimental Research Site (Wisconsin, USA) that tested the effects of canopy openings alone on the SMC abundance and soil respiration along the gap gradient. Soils were sampled in four treatments (gaps, gaps + DWD addition, control + DWD addition and a control), and SMC abundance and composition were quantified using a modified phospholipid fatty acid (PLFA) and fatty acid methyl ester (FAME) method. Our analyses indicated a stronger response of the SMC to within-gap microenvironments than to the stand-level interaction of DWD addition and canopy openings. We found significant variation in the SMC along the north–south transect within the gaps, with higher abundance of arbuscular mycorrhizal fungi, soil temperature, unsaturation bacterial stress ratio and lower bacterial abundance in the northern portion of the canopy openings. DWD addition within gaps buffered the soil from extreme temperature changes while increasing gram-positive bacteria abundance that tend to rely on recalcitrant carbon sources and are more resistant to environmental stress. These patterns indicate that gap openings and DWD addition increased soil microenvironmental spatial heterogeneity and suggest that structural complexity may contribute to carbon storage by promoting sequestration in regenerating vegetation and by shaping the SMC to favor greater C use efficiency.