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• Five land uses were assessed for soil organic carbon (SOC) dynamics. • Conversion of forest land to cropland declined SOC and biological activities. • Alder + large cardamom land use was a viable alternative for SOC buildup. • Alder + large cardamom land use increased the recalcitrant pool of SOC fractions. Land use management exerts a tenacious impact on soil organic carbon (SOC) dynamics; however, the impact varies with climate, soils, and management practices. Therefore, an in-depth understanding of changes in SOC pools and its fractions is necessary to reduce carbon (C) emissions and adopt efficient land use planning for sustainable soil management in the North Eastern Himalayan (NEH) region of India. The soils under five prominent land uses [e.g., alder (Alnus nepalensis) + large cardamom (Amomum subulatum), alder + turmeric (Curcuma longa), ginger (Zingiber officinale) + maize (Zea mays), ginger and undisturbed forest] were sampled down to 45 cm depth to assess the impacts of land use systems on SOC content and storage, its fractions, microbial biomass carbon (MBC) and the dehydrogenase (DHA) activities. Results demonstrated that undisturbed forest soil had the highest organic carbon (OC, 145.8 Mg ha−1), active C (AC, 73.7 Mg ha−1), passive C (PC, 72.1 Mg ha−1) pools, MBC and DHA activities followed by alder + large cardamom system (140.7 Mg OC ha−1, 70.9 Mg AC ha−1, and 69.8 Mg PC ha−1, respectively). The soils under undisturbed forest and alder + large cardamom system had a higher share of the very labile C fractions for all depths than other land uses. Conversely, soils under sole ginger and ginger + maize land uses had a greater proportion of non-labile C (NLC) fractions; however, absolute values of the NLC pool were the highest under undisturbed forest soil. Alder + large cardamom land use system had the highest AC: PC pool ratio (1.13) and C stratification (1.02–1.05) compared to the other land uses. Of the various land uses, SOC pools (0–45 cm) in six years were reduced nominally under alder + large cardamom system (4.2%), while the reduction was maximum under the ginger system (11.2%) as compared to the SOC pools of undisturbed forest. The study demonstrated that the cultivation of crops like maize and/or ginger is more degrading and will always have a negative impact on the fertility and overall health of the Himalayan soil. Hence, alder + large cardamom system may be promoted to restore the soil C in the Sikkim Himalayan region of NEH, India, and other similar regions of the world. [ABSTRACT FROM AUTHOR]