Abstract We examine the implementation of ambient noise array tomography in an urban environment to assess the 3D near-surface shear wave velocity (VS) structure at an intermediate spatial scale (∼1 km2, depth range 200–300 m). The application employs cross correlation traces of vertical component ambient noise recordings from a local network installed in Thessaloniki city (Northern Greece), allowing the determination of Rayleigh wave travel times for the frequency range of 1.5–14 Hz. The results confirm the presence of a complex subsurface with strong lateral variations in the geology, with travel times varying up to almost one order of magnitude. A surface wave travel time tomography approach was applied for each frequency to determine the spatial variability of the group velocity, involving the use of approximate Fresnel volumes, as well as damping and spatial smoothing constraints to stabilize the results. We also employed an interfrequency smoothing scheme to obtain smooth but data-compatible dispersion curves at the cost of inverting all travel time data simultaneously. Following the application of several quality cutoff criteria, we reconstructed local group slowness dispersion curves for a predefined tomographic grid in the study area. The final 3D velocity model was determined by a modified Monte Carlo inversion of these dispersion curves and the spatial integration of the obtained 1D VS profiles. Different model parameterizations were tested for the inversion to determine the optimal datafit. The final 3D velocity model is in a very good agreement with the local geology, previous larger scale studies, and other geophysical surveys, providing additional structural constraints (such as hidden fault identification) for the complex sedimentary deposits and bedrock formation in Thessaloniki, up to the depth of ∼250–300 m. The introduction of the aforementioned modifications to the ambient noise array tomography suggests that it can be efficiently adjusted and employed as a reliable tool for imaging the 3D seismic structure in urban environments with complex geology.