The indigenous farming systems in the state of Sikkim state are by and large based on organic farming. These systems facilitate the build-up of soil organic matter, reduce risk of erosion and runoff, and enhance nutrient storage in soils for plant. The traditional/cultural knowledge of the mountain societies is the inherent identity that is embedded within each ethnic community, which is very unique. The indigenous integrated organic nutrient management practices have resulted in high fertility status of acidic soils compared to other states of northeastern region particularly in respect of P fertility. Such indigenous technologies also resulted in sustainable soil health for achieving optimum crop yield, adequate water management, and healthy plant protection measures. Terrace farming is tradition in the hilly state, which reduces the runoff and sediment by 41.9% and 52%, respectively, and enhances grain yields and soil moisture content by 44.8% and 12.9%, respectively. Being organic-based farming at large, all the crops are grown with high doses of FYM, vermicompost, and green manuring, resulting in almost 100% reduction in synthetic fertilizers. Also, the insect pest control is done by indigenous methods like neem extract spray, agave extract, neem cake application, seed treatment with cow urine, wood ash, and kerosene which eliminate the 100% use of market-purchased chemicals. Crop mulching with leaves and twigs of various forest trees, weeds, grasses available around the field, animal bedding, and surplus-rich straw, amounting to 5–20 t/ha on dry basis, is a common practice that increases the crop yields and soil moisture retention to the extent of 40–55%. Blending of ITKs with modern scientific technologies is the need of the day to support sustainable development of organic agriculture and allied sector. Hence, need-based doable technologies have been suggested for soil, water, and plant management to reduce the cost of production (without sacrificing crop yields), improve soil health, enhance input use efficiency, improve environment, conserve water, etc.