Resolving the status of soil carbon with land cover is critical for addressing the impacts of climate change arising from land cover conversion in boreal regions. However, many conventional inferential approaches inadequately gauge statistical significance for this issue, due to limited sample sizes or skewness of soil properties. This study aimed to address this drawback by adopting inferential approaches suitable for smaller samples sizes, where normal distributions of soil properties were not assumed. A two-step inference process was proposed. The Kruskal–Wallis (KW) test was first employed to evaluate disparities amongst soil properties. Generalized estimating equations (GEEs) were then wielded for a more thorough analysis. The proposed method was applied to soil samples (n = 431) extracted within the southern transition zone of the boreal forest (49°–50° N, 80°40′–84° W) in northern Ontario, Canada. Sites representative of eight land cover types and seven dominant tree species were sampled, investigating the total carbon (C), carbon-to-nitrogen ratio (C:N), clay percentage, and bulk density (BD). The KW test analysis corroborated significance (p-values < 0.05) for median differences between soil properties across the cover types. GEEs supported refined robust statistical evidence of mean differences in soil C between specific tree species groupings and land covers, particularly for black spruce (Picea mariana) and wetlands. In addition to the proposed method, the results of this study provided application for the selection of appropriate predictors for C with digital soil mapping.