This paper presents the identification of the instantaneous modal properties and the experimental response of a full-scale, five-story base-isolated RC building tested on a shake table. A suite of earthquake motions of various intensities was applied to the building to progressively increase the seismic demand. The deterministic-stochastic subspace identification method is employed to estimate the variations of the modal properties of the building by employing a short-time windowing approach. The changes of the modal parameters during the seismic motions are tracked and analyzed. Observed and measured responses of the structure are analyzed and correlated with the variation of the identified modal parameters. The nonlinear behavior of the isolators generates the variation of the identified natural frequencies and equivalent damping ratios of the building, which change in agreement with the input motion intensity. A high correlation between the effective stiffness of the isolators and the instantaneous frequency of the first mode is found. The effective damping ratio of the isolation system and the instantaneous damping ratio of the fundamental mode of the building are highly correlated.