This study explored the opportunities for the retention and return of nutrients in local bio-energy production using energy crops (oil palm, jatropha and cassava), fuel wood, manure, rice husks and a common pest plant (water hyacinth). For all bio-energy systems some return of nutrients is possible, but the differences between conversion technologies and between feed stocks can be large. Anaerobic digestion retains most nutrients, while combustion and gasification loses all nitrogen. Palm oil has the lowest potential for nutrient return of the energy crops; however it is the most efficient, together with cassava, regarding the required nutrient input per mega joule of bio-energy. Jatropha is the least efficient energy crop, it requires the most nutrients to produce a mega joule of energy