This paper focuses on a geophysical-based analysis of the soils in Arica and Iquique, both main cities in northern Chile. The large seismogenic coupling and the 136-year seismic gap predispose the north of the country to the highly likely seismic activity that could affect this area. This seismotectonic scenario highlights the importance of the assessment of earthquake hazards in urban domains. In this context, seismic microzoning emerges as a tool to identify areas that are more or less susceptible to ground motion amplification. In both cities, 148 sites were chosen to perform geophysical surveys based on surface wave methods, namely the spatial autocorrelation, frequency-wave number and H/V spectral ratio techniques. By inverting the measurements, local shear wave velocity profiles and predominant frequencies were derived. Additionally, seven boreholes were drilled to further complement the gathered data. With the available results, the cities were subdivided into different zones with similar properties in terms of the average shear wave velocity on the upper 30 m ( V30sVs30 ) and the predominant site’s frequency F0F0 ; these were parameters that were found consistent with the geology of each city. The collected information suggests zones that are more prone to ground motion amplification, namely: the northern side of Arica, the south-east area of Iquique, the northern limit of Iquique and the artificial landfill of the port of Iquique. The microzoning was compared to the ground motion records of the April 1, 2014, Iquique earthquake and showed to be consistent with the expected motion amplification in Iquique.