Quito, the capital city of Ecuador, with a population close to three million inhabitants, is located in an earthquake‐prone region that has been struck by important events in the past. The city is built on the hanging wall of an active reverse fault, constituting a piggy‐back basin filled with volcanic and fluvial origin deposits. To date, the Quito basin deep structure remains unknown as well as its effect on amplification of seismic waves. Since 2009, a permanent accelerometric network has been deployed in the city (Red Nacional de Acelerógrafos de Quito at present 18 stations) and operates in continuous recording mode. We select the 179 best‐recorded earthquakes and estimate the horizontal‐to‐vertical and the standard spectral ratios to highlight site effects in the basin. We find that the southern part of the basin presents a strong site amplification at low frequencies (peak around 0.35 Hz with an amplitude larger than 3) that is not present in the northern part. The recordings of the 16 April 2016 7.8 Pedernales earthquake that occurred on the subduction interface 150 km away from Quito confirm this low‐frequency amplification in the southern part of the city, by observing larger amplitudes and longer durations of the signals. Higher frequencies (around 4 Hz) are also amplified at given sites, but they are spatially more variable.