The present study applies the spectral inversion method, proposed by Iwata and Irikura (1986, 1988), to separate the source, propagation path, and local site effects from observed strong motion records in the frequency range from 0.5 to 10 Hz for the analyses of the relationship between the local subsurface conditions and the local site amplifications in some areas of Lima city, Peru. The analyzed data are S-wave portions of accelerograms in horizontal components observed at 5 stations for 11 events recorded along the Pacific coast of Lima city. These events are superficial and intermediate earthquakes with local magnitudes (ML) from 4.0 to 5.7 and with hypocentral distances from 40 to 180 km. From the spectral inversion, solutions for source spectra, inelasticity factor of propagation path for S-wave (QS-value), and site amplification factor at each site are obtained. The factors of site amplification Gj(f) obtained in the present study are compared with the results obtained by Cabrejos (2009) for stations CSM, CAL, MOL and CDLCIP employing the standard spectral ratio (SSR) method, which support our results especially at frequencies below 5 Hz. QS-value obtained shows frequency dependency of the form QS(f)=80.4f0.63. In addition, the influence of non-linearity on the site response is evaluated during the Pisco earthquake which it is concluded that nonlinear response of the soils was not detected at acceleration levels below 115.2 gal (the maximum peak ground acceleration recorded in Lima city). The study also proposed relationships between the amplifications with average S-wave velocity in top 30 meters of the S-wave profiles for some stations at each frequency.