SUMMARY Strong ground shaking has the potential to generate significant dynamic strains in shallow materials such as soils and sediments, thereby inducing nonlinear site response resulting in changes in near-surface materials. The nonlinear behaviour of these materials can be characterized by an increase in wave attenuation and a decrease in the resonant frequency of the soil; these effects are attributed to increased material damping and decreased seismic wave propagation velocity, respectively. This study investigates the ‘in-situ’ seismic velocity changes and the predominant ground motion frequency evolution during the 2016 Kumamoto earthquake sequence. This sequence includes two foreshocks (Mw 6 and Mw 6.2) followed by a mainshock (Mw 7.2) that occurred 24 hr after the last foreshock. We present the results of the seismic velocity evolution during these earthquakes for seismological records collected by the KiK-net (32 stations) and K-NET (88 stations) networks between 2002 and 2020. We analyse the impulse response and autocorrelation functions to investigate the nonlinear response in near-surface materials. By comparing the results of the impulse response and autocorrelation functions, we observe that a nonlinear response occurs in near-surface materials. We then quantify the velocity reductions that occur before, during, and after the mainshock using both approaches. This allows us to estimate the ‘in-situ’ shear modulus reduction for different site classes based on V$_{S30}$ values (V$_{S30}\lt 360$ m s−1, $360\lt $V$_{S30}\lt 760$ m s−1 and V$_{S30}\gt 760$ m s−1). We also establish the relationships between velocity changes, shear modulus reduction, variations in predominant ground motion frequencies and site characteristics (V$_{S30}$). The results of this analysis can be applied to site-specific ground motion modelling, site response analysis and the incorporation of nonlinear site terms into ground motion models.