The new technologies in the field of food processing provide the opportunity to revive some productions that are crushed by the global market and environmental issues. However in the citrus sector the lack of investment and difficulties to manage economic cost are likely to slow down the take-off of these innovations. Starting from the results of the 7FP European Project NAMASTE, this paper provides a methodology for the computation of the full cost of several citrus by-products and an attempts to analyse through a simulation model the decision making problem of a citrus firm who decide to upgrade citrus waste in order to obtain several by-products. The results show the importance of using the full cost in the management of resources. However, the possibility of producing from citrus wastes are constrained by production capacity resources and by the overall efficiency of production technologies. The economic sustainability can be achieved by an increases in production efficiency, improving the technologies and the ability to reuse waste. However, a large amount of investment is still required, which only the large firms can support, at least in the short term.