The soil microbiome determines the fate of plant-fixed carbon. The shifts in soil properties caused by land use change leads to modifications in microbiome function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated using metaproteomics, metabarcoding, and a 13C-labeled litter decomposition experiment across two temperate sites with differing soil pH each with a paired land use intensity contrast. 13C incorporation into microbial biomass increased with land use intensification in low-pH soil but decreased in high-pH soil, with potential impact on carbon use efficiency in opposing directions. Reduction in biosynthesis traits was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. We observed divergent pH-controlled pathways of SOC cycling. In low-pH soil, land use intensification alleviates microbial abiotic stress resulting in increased biomass production but promotes decomposition and SOC loss. In contrast, in high-pH soil, land use intensification increases microbial physiological constraints and decreases biomass production, leading to reduced necromass build-up and SOC stabilization. We demonstrate how microbial biomass production and respiration dynamics and therefore carbon use efficiency can be decoupled from SOC highlighting the need for its careful consideration in managing SOC storage for soil health and climate change mitigation.