The Marine Strategy Framework Directive intends to adopt ecosystem-based management for resources, biodiversity and habitats that puts emphasis on maintaining the health of the ecosystem alongside appropriate human use of the marine environment, for the benefit of current and future generations. Within the overall framework of ecosystem-based management, ecosystem models are tools to evaluate and gain insights in ecosystem properties. The low data availability and complexity of modeling deep-water ecosystems has limited the application of ecosystem models to few deep-water ecosystems. Here, we aim to develop an ecosystem model for the deep-sea and open ocean in the Azores exclusive economic zone with the overarching objective of characterizing the food-web and structure of the ecosystem. An ecosystem model with 45 functional groups, including a detritus group, two primary producer groups, eight invertebrate groups, 29 fish groups, three marine mammal groups, a turtle and a seabird group was built. Overall data quality measured by the pedigree index was estimated to be higher than the mean value of all published models. Therefore, the model was built with source data of an overall reasonable quality, especially considering the normally low data availability for deep-sea ecosystems. The total biomass (excluding detritus) of the modeled ecosystem for the whole area was calculated as 24.7 t km−2. The mean trophic level for the total marine catch of the Azores was estimated to be 3.95, similar to the trophic level of the bathypelagic and medium-size pelagic fish. Trophic levels for the different functional groups were estimated to be similar to those obtained with stable isotopes and stomach contents analyses, with some exceptions on both ends of the trophic spectra. Omnivory indices were in general low, indicating prey speciation for the majority of the groups. Cephalopods, pelagic sharks and toothed whales were identified as groups with key ecological roles in the ecosystem. Due to concerns on the use of ecosystem models with low confidence in exploring management decisions and ecological theories, the current version of this model should only be use with caution until biomass estimates are validated with survey data or the model is fitted to time series.