The fate of benzo(a)pyrene (BaP), a ubiquitous contaminant reported to be persistent in the environment, is largely controlled by its interactions with the soil organic matter. In the present study, the spectral characteristics of fluorophores present in the physical fractions of the soil organic matter were investigated in the presence of pure BaP solution. After extraction of humic substances (HSs), and their fractionation into fluvic acid (FA) and humic acid (HA), two fluorescent compounds (C1 and C2) were identified and characterized in each physical soil fraction, by means of fluorescence excitation-emission matrices (FEEMs) and Parallel Factor Analysis (PARAFAC). Then, to each type of fraction having similar DOC content, was added an increasing volume of pure BaP solution in attempt to assess the behavior of BaP with the fluorophores present in each one. The application of FEEMs-PARAFAC method validated a three-component model that consisted of the two resulted fluorophores from HSs, FA and HA (C1 and C2) and a BaP-like fluorophore (C3). Spectral modifications were noted for components C2HSs (C2 in humic substances fraction) (λex/λem: 420/490–520 nm), C2FA (C2 in fulvic acid fraction) (λex/λem: 400/487(517) nm) and C1HA (C1 in humic acid fraction) (λex/λem: 350/452(520) nm). We explored the impact of increasing the volume of the added pure BaP solution on the scores of the fluorophores present in the soil fractions. It was found that the scores of C2HSs, C2FA, and C1HA increased when the volume of the added pure BaP solution increased. Superposition of the excitation spectra of these fluorophores with the emission spectrum of BaP showed significant overlaps that might explain the observed interactions between BaP and the fluorescent compounds present in SOM physical fractions.