As tools within ecosystem-based fisheries management (EBFM), a wide range of Ecosystem Models (EMs) have been designed to represent ecosystem complexity, but it is not always clear how the outputs of these models can be applied. We address this debate in a literature review to illustrate how a better understanding of ecosystem modeling within the EBFM framework could facilitate the use of EMs in the decision-making process. We classify EMs according to their complexity, and qualitatively evaluate their level of success with regard to five general goals of EBFM. In principle, no single EM is found to successfully accomplish all the EBFM goals. Therefore, we suggest that the way in which ecosystem modeling can effectively contribute to EBFM is through a structured modeling process, which should be pursued according to the context of each specific area. Within this planning strategy a range of Ems should be considered, from rather simple ones with few parameters, whose outputs are scientifically robust but possibly of limited use within the EBFM, to those which include a large number of ecosystem elements yet at the expense of increased uncertainty. If multiple EMs, despite their different assumptions, leads to consistent and converging results then robust management decisions will be supported. The present paper appears particularly useful to anyone confronted with the selection of modeling tools for the implementation of fisheries management strategies considering the particular situation of the fishery.