Understanding the complex interplay among altitudinal gradients, tree species diversity, structural attributes, and soil carbon (C) is critical for effective coniferous forest management and climate change mitigation. This study addresses a knowledge gap by investigating the effects of altitudinal gradient on coniferous tree diversity, biomass, carbon stock, regeneration, and soil organic carbon storage (SOCs) in the understudied temperate forests of the Hindu-Kush Kalam Valley. Using 120 sample plots 20 × 20 m (400 m²) each via a field inventory approach across five altitudinal gradients [E1 (2000–2200 m)–E5 (2801–3000 m)], we comprehensively analyzed tree structure, composition, and SOCs. A total of four coniferous tree species and 2172 individuals were investigated for this study. Our findings reveal that elevation indirectly influences species diversity, SOCs, and forest regeneration. Notably, tree height has a positive relationship with altitudinal gradients, while tree carbon stock exhibits an inverse relationship. Forest disturbance was high in the middle elevation gradients E2–E4, with high deforestation rate at E1 and E2. Cedrus deodara, the dominant species, showed the highest deforestation rate at lower elevations (R² = 0.72; p < 0.05) and regeneration ability (R² = 0.77; p < 0.05), which declined with increasing elevation. Middle elevations had the highest litter carbon stock and SOCs values emphasizing the critical role of elevation gradients in carbon sink and species distribution. The regeneration status and number of trees per ha in Kalam Valley forests showed a significant decline with increasing elevation (p < 0.05), with Cedrus deodara recording the highest regeneration rate at E1 and Abies pindrow the lowest at E5. The PCA revealed that altitudinal gradients factor dominate variability via PCA1, while the Shannon and Simpson Indices drives PCA2, highlighting ecological diversity’s independent role in shaping distinct yet complementary vegetative and ecological perspectives. This study reveals how altitudinal gradients shape forest structure and carbon sequestration, offering critical insights for biodiversity conservation and climate-resilient forest management.