After the 2009 L’Aquila 6.1 earthquake, particular attention was paid to the large difference of Mercalli–Cancani–Sieberg (MCS) macroseismic intensity between the nearby villages of Onna (9.5 MCS) and Monticchio (6 MCS). Several authors estimated that in Onna, settled in the Aterno river valley, ground motions were amplified at 2–3 Hz by up to a factor of 5 with respect to Monticchio, settled on more competent rocks. Although there was a general agreement that the spectral peak was caused by the resonance of the uppermost 40 m layer, a satisfactory fit of the amplitudes was not provided. Here, we apply spectral ratio techniques to 1437 aftershock seismograms (magnitude between 1.8 and 3.9) to compare ground motions within Onna and between Onna and Monticchio. Spectral amplitudes at stations located outside and inside the “red zone” of Onna show that the seismic response was uniform, confirming that vulnerability was crucial for the heavier damage of the ancient part of the village. We have also estimated the empirical transfer function of Onna through the spectral ratios between Onna and Monticchio. Although in a 1D simplification, a model with a further velocity contrast of at 200 m of depth produces a more accurate fit of observations. Using the new velocity profile, we modeled the mainshock ground motion at Onna in an equivalent‐linear approach. Accelerations are amplified by a factor of 2 and spectral ordinates increase from at 0.2 s to at 0.5 s, a shaking level that can be destructive for nonductile ancient buildings. This study shows that accurate estimates of empirical transfer functions, even in a simplified 1D approach, provide useful constraints to the deeper velocity structure where measurements are shallow or lacking.