Biophysical and energy analyses of an agro-ecosystem are necessary for effective and efficient production planning. The present paper deals with biophysical, economic and energy input–output analyses of different agro-ecosystems and energy flows of village ecosystem in the Garhwal Himalaya. Vegetable based agro-ecosystem was profitable in high-hills, whereas wheat, rice, soybean and barnyard millet based agro-ecosystems proved energetically output–input efficient in lower hill farming system. The annual net energy contribution to the village ecosystem ranged between 4275 and 13,793 GJ from crops, 7427 and 11,834 GJ from forest and 2550 and 3690 GJ from the market. The gain of energy from the system to human beings was 8313–11,273 GJ and to livestock 6009–18,566 GJ per village per annum. Forest provided the maximum energy support to the village ecosystem, whereas crops proved the second major source of energy. This indicates the exploitable potential of these two components through adoption of scientific crop production and proper forest management practices in the Garhwal Himalaya.