Pedodiversity is generally neglected in studies concerning soil organic carbon (SOC). Therefore, this investigation aimed to explore the effect of soil types on the following: (1) soil processes related to organic matter (OM) dynamics along the profile; and (2) the microbial community and functionality within the uppermost horizon. Humic Dystrudepts (HD), Typic Dystrudepts (TD), and Humic Lithic Dystrudepts (HLD) were selected in beech forests of the Apennine ridge in the Emilia-Romagna Region (Italy). Soils were sampled by horizons until parent material, and physico-chemical and functional analyses were performed. The results showed that both HD and HLD soils had a higher SOC accumulation than TD, particularly within the deeper horizons. Such accumulation might be due to the lower turnover rate of soil OM forms, namely fulvic acid-like substances, humic acid-like substances, and non-extractable OM. Noteworthy, the A horizons showed slight differences in SOC among the soil types, suggesting similar SOC decomposition processes. This fact was confirmed by the lack of differences in microbial DNA-based diversity and functionality. This study highlighted the importance of combining pedodiversity and microbial diversity for a wider perspective on SOC dynamics.