Physical analysis of in situ fire experiments on soils are useful for the estimation of subsurface thermal diffusivity, which is affected by factors such as water, heterogeneity and heating conditions. To address the uncertainties due to these factors, a new data‐processing procedure based on inverse methods was developed and experimentally applied to soils from an archaeological site in the Atacama Desert, Chile. By combining experimental data and numerical simulations, we determined the dominant physical processes arising during the heating. The analysis succeeded in defining practical procedures to obtain a more accurate estimation of the diffusivities, thus reducing the above‐mentioned uncertainties.