Querétaro city is situated in the north central part of the Trans-Mexican Volcanic Belt, and it was considered by several previous studies as an aseismic region. Since that, as well as considering the surrounding seismotectonic setting, it was significant to assess the seismic hazard across the city which aids in the development and updating the building codes and the seismic design criteria. In this regard, the Horizontal to Vertical Spectral Ratio (HVSR) Nakamura's technique has been applied to investigate the local-site effects across the city. Microtremor measurements were performed at 76 free-field selected sites, through the implementation of portable seismic stations equipped with three-component velocity sensors of Trillium Compact 120 s broadband seismometer. Then, acceleration values were estimated by generating synthetic accelerograms based on a recently-developed algorithm that combines the HVSR technique and the theory of random vibrations, considering as a reference the September 19, 2017 (Mw 7.1) intraslab earthquake recorded at the Centro de Geociencias (CGEO) Seismic Station, in Juriquilla, Querétaro. Finally, by computing the pseudoacceleration response spectra through the linear acceleration method at structural periods of 0.1, 0.5, 1.0, 2.0, and 5.0 s, corresponding seismic hazard maps were established for the studied region. Based on these values and delimiting the areas with higher risk considering the interaction of the soil with the buildings on it, this article is the basis for delimiting seismic parameters that define the city, with future applications in the seismic engineering considering both linear and nonlinear structural behaviors.