Crop productivity is directly dependent on soil fertility. High organic carbon content in soil is vital as it leads to improved soil quality, increased productivity, and stable soil aggregates. In addition, with the signing of the climate agreement, there is growing interest in carbon sequestration in landscapes. This paper looks at how soil organic carbon (SOC) can be increased so that it contributes not only to the reduction of atmospheric CO2, but also translates to the increased food production, thereby enhancing food security. This synergy between climate change mitigation and enhancing food security is even more relevant for mountain landscapes of the Hindu Kush Himalayan (HKH) region where there remains huge potential to increase CO2 sequestration and simultaneously address food security in the chronic food deficit villages. Soil samples were collected from seven transects each in Bajhang and Mustang and from four land use types in each transect. Samples of soils were taken from two depths in each plot: 0–15 cm and 15–30 cm below the soil surface to compare the top soil and subsoil dynamics of the soil nutrients. The lab analysis was performed to assess the soil texture, soil acidity in “power of hydrogen” (pH), and macro-nutrients reflecting soil fertility. Secondary data was used to analyze the level of food deficit in the villages. The pH value of soil from Bajhang ranged from 5.3 to 9.1. The pH value of soil ranged from 5.7 to 8.8 in Mustang. SOC contents of sampled soils from Bajhang ranged from 0.20% to 7.69% with a mean amount of 2.47% ± 0.17%. SOC contents of sampled soils from Mustang ranged from 0.51% to 8.56% with a mean amount of 2.60% ± 0.25%. By land use type, forest land had the highest carbon (C) content of 53.61 t·ha−1 in Bajhang, whereas in Mustang, agricultural land had the highest C content of 52.02 tons·ha−1. Based on these data, we can say that there is potential for increasing SOC through improved soil health and crop production holistic soil management should be practiced for higher productivity, and incorporating livestock for farmyard manure would fertilize cultivated soils, which increases soil productivity. Increasing productivity would aid in enhancing the access and availability of food in these mountain villages.