Soil organic carbon (SOC) represents a major terrestrial carbon pool, yet the processes that regulate its storage remain uncertain, particularly in water-limited ecosystems. The behavior of SOC is informed by partitioning into mineral-associated organic carbon (MAOC), considered more persistent, and particulate organic carbon (POC), which is more labile. We investigated how SOC fractions were affected by forest tree species, including <em>Pinus halepensis</em> (a canopy conifer), <em>Quercus calliprinos</em> (a sub-canopy broadleaf), and <em>Pistacia lentiscus</em> (an understory woody shrub) as compared to mixing of these species, focusing on shallow-soil mature Mediterranean stands. To elucidate further insights, the effects of soil physicochemical properties and microbial community were examined. Across soil samples, SOC concentrations were up to twofold higher under tree canopies compared to forest gaps with <em>Quercus</em> plots storing 10–30% more SOC than <em>Pinus</em> and <em>Pistacia</em> plots. SOC variation was primarily explained by POC, for which mixed plots showed increased concentrations as compared to monospecific plots. In contrast, MAOC displayed a saturation pattern (maximum ~45 g C kg⁻¹ soil), strongly constrained by clay and silt content, with apparent high saturation levels. Mixed forests supported seasonally stable microbial communities but did not consistently increase microbial diversity. Bacterial composition was shaped by microsite conditions, with soils under tree canopies harboring subsets of the more diverse forest-gap communities. Overall, despite the fact that mixed forest increased microbial richness, this effect did not propagate to affect the different soil C pools. Nevertheless, the effect of forest type on soil C pools was modulated by specific microsites and tree-species characteristics. For instance, transitioning to mixed forests could increase SOC by approximately 6.1 Mg C ha⁻¹ compared to monospecific pine forests, but this carbon is expected to primarily be stored in the labile POC pool, especially in soils near saturation.