Lisbon’s historical seismicity, socioeconomic importance and population density contribute to a moderate to high seismic risk. The geological setting of the city includes cases of inclined layers, interbedding sedimentary rock layers in soil deposits, sand and clay layers in the same geological unit, leading to cases of shear wave velocity inversion and a large scatter of geotechnical properties within each geological unit. The morphological setting of the city is characterised by the existence of several hills and relatively shallow, stream-carved valleys filled with alluvial deposits. The seismic site effects in Lisbon were assessed through numerical simulation using the linear equivalent method and adopting the two types of seismic action defined in the Portuguese National Annex of Eurocode 8: (i) one-dimensional subsoil models covering the city, at sites where borehole data and geophysical data were available; (ii) two-dimensional subsoil models along three cross-sections representative of the geological settings and morphology. The distribution of amplification factors in the city revealed a pattern related to ground characteristics that impact seismic soil response, such as the presence of high-thickness cover deposits, significant shear-wave variations, alluvial valleys, a crest or significant slope variations and inclined layers. The 2D/1D spectral ratio highlighted the areas were 2D seismic effects are more important. The soil factor determined in the numerical analyses was consistently greater than the soil factor values indicated in Eurocode 8.