Spectroscopic non-destructive methods have high potentialities as fast, cheap and easy-to-be-used approaches to address olive oil quality and authenticity. Based on previous research where near-UV Visible spectroscopy was used to investigate extra-virgin olive oils (EVOOs) and their main pigments’ content (i.e., β-carotene, lutein, pheophytin a and pheophytin b), we have implemented the spectral deconvolution method in order to follow the EVOO’s life, from ‘freshly pressed’ to ‘on-the-shelf’ EVOO samples at different storage time. In the first part of the manuscript, the new implemented deconvolution spectroscopic method aimed to quantify two additional pigments, namely chlorophyll a and chlorophyll b, is described and tested on ‘ad hoc’ samples with known concentrations of chlorophylls. The effect of light exposure and acidification was investigated to test the reliability and robustness of the spectral deconvolution. In the second part of the work, this approach was used to study the kinetic of pigments’ degradation in several monocultivar fresh EVOO samples under optimal storage’s conditions. The results here reported show that this spectroscopic deconvolution approach is a good method to study fresh EVOOs too; moreover, the proposed method revealed to be sensitive to detect eventual stresses of olive oil samples stored in not-good conditions.