Forest harvesting and the associated loss of nutrients and carbon has the potential to negatively affect the soil microbial community, which plays a significant role in the health and productivity of the forest ecosystem. We used an experiment to evaluate the effects of group selection using whole-tree harvesting on the soil microbial community in a second growth northern hardwood forest dominated by sugar maple (Acer saccharum Marsh.) in northern Wisconsin, USA. We compared the response of the soil microbial community in 200 m2 and 380 m2 harvested gaps to unharvested controls during the spring and summer in the first two years post-harvest, and continued to monitor changes in the soil microbial communities and microenvironment in 380 m2 gaps in years four, five, and seven post-harvest. Changes in community size and composition were assessed using phospholipid fatty acid (PLFA) analysis. We found that the abundance of arbuscular mycorrhizal fungi initially decreased following harvest, while abundance of anaerobic and gram positive bacteria, and the cyclo/pre-cyclo microbial stress ratio increased; responses that can be linked to microclimatic variability and resource accessibility. Neither actinomycete bacteria nor saprotrophic fungi exhibited an initial response to harvest, but in later years, we observed a decrease in actinomycetes and an increase in fungal abundance, suggesting a competitive interaction between the two main complex carbon-utilizing microbial groups. Canopy gap size had a minimal effect on the soil microbial community, resulting in a higher microbial stress ratio in 200 m2 gaps. The microbial community exhibited seasonal and yearly fluctuation, which reinforces the need for repeated sampling over multiple seasons to correctly interpret management effects. Despite the large amount of seasonal and yearly variability, we began to see signs of recovery in the soil microbial community between two and four years post-harvest. We conclude that group selection accomplished via whole-tree harvesting of this size and scale does not result in long-term effects on the soil microbial community in this temperate northern hardwood forest.