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Abstract Background Land use and land cover changes have a significant impact on the dynamics of soil organic matter (SOM) and its fractions, as well as on overall soil health. This study conducted in Bharatpur Catchment, Chitwan District, Nepal, aimed to assess and quantify variations in total soil organic matter (TSOMC), labile organic matter fraction (CL), stable organic matter fraction (CS), stability ratio (SR), and carbon management index (CMI) across seven land use types: pastureland, forestland, fruit orchards, small-scale conventional agricultural land, large-scale conventional agricultural land, large-scale alternative fallow and conventional agricultural land, and organic farming agricultural land. The study also explored the potential use of the Carbon Management Index (CMI) and stability ratio (SR) as indicators of soil degradation or improvement in response to land use changes. Results The findings revealed significant differences in mean values of TSOMC, CL, and CS among the different land use types. Forestland and organic farming exhibited significantly higher TSOMC (3.24%, 3.12%) compared to fruit orchard lands (2.62%), small scale conventional farming (2.22%), alternative fallow and conventional farming (2.06%), large scale conventional farming (1.84%) and pastureland (1.20%). Organic farming and Forestland also had significantly higher CL (1.85%, 1.84%) and CS (1.27%, 1.39%) compared to all other land use types. Forest and organic farming lands showed higher CMI values, while pastures and forests exhibited higher SR values compared to the rest of the land use types. Conclusions This study highlights the influence of various land use types on soil organic matter pools and demonstrates the potential of CMI and SR as indicators for assessing soil degradation or improvement in response to land use and land cover changes.