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Biogas production from organic by-products is a way to recover energy and nutrients. However, biogas production is not the only possible conversion alternative for these by-products, and hence there is interest in studying how organic by-products are treated today and which alternatives for conversion are the most resource efficient from a systems perspective. This paper investigates if biogas production is a resource efficient alternative, compared to business as usual, to treat food industry by-products, and if so, under what circumstances. Five different cases of food industries were studied, all with different prerequisites. For all cases, three different scenarios were analysed. The first scenario is the business as usual (Scenario BAU), where the by-products currently are either incinerated, used as animal feed or compost. The second and third scenarios are potential biogas scenarios where biogas is either used as vehicle fuel (Scenario Vehicle) or to produce heat and power (Scenario CHP). All scenarios, and consequently, all cases have been analysed from three different perspectives: Economy, energy, and environment. The environmental perspective was divided into Global Warming Potential (GWP), Acidification Potential (AP), and Eutrophication Potential (EP). The results show, in almost all the systems, that it would be more resource efficient to change the treatment method from Scenario BAU to one of the biogas scenarios. This paper concludes that both the perspective in focus and the case at hand are vital for deciding whether biogas production is the best option to treat industrial organic by-products. The results suggest that the food industry should not be the only actor involved in deciding how to treat its by-products.