To assess the health condition of structures and infrastructure during their service lives, continuous vibration-based monitoring represents a viable and cost-effective solution. Model updating and digital twins are increasingly adopted for damage detection. However, significant gaps and uncertainties in damage quantification still arise. This work presents original data from output-only modal identification tests on full-scale, two-storey reinforced concrete (RC) frames subjected to pseudo-dynamic loading to simulate seismic damage. The frames are tested with two masonry infill wall configurations with three-sided and four-sided boundary conditions, and the observed seismic damage is correlated to a damage scale. Output-only modal identification tests are performed before and after testing to catch variations in modal properties due to observed damage. Experimental data are used to build a refined finite element model able to reliably simulate the static and dynamic performance of the infilled RC frames before and after damage. The model allowed for the further assessment of the variation in natural frequencies of tested specimens at different earthquake intensities, the correlation of such variations to damage levels, and identification of the contribution of structural and non-structural components to the overall frequency variation.