The environmental effects of agriculture and food are much discussed, with competing claims concerning the impacts of conventional and organic farming. Life cycle assessment (LCA) is the method most widely used to assess environmental impacts of agricultural products. Current LCA methodology and studies tend to favour high-input intensive agricultural systems and misrepresent less intensive agroecological systems such as organic agriculture. LCA assesses agroecological systems inadequately for three reasons: (1) a lack of operational indicators for three key environmental issues; (2) a narrow perspective on functions of agricultural systems; and (3) inconsistent modelling of indirect effects.