This is our follow-up study carried out in an order to collect experimental evidence regarding the impact of heavy water (D2O) on the spontaneous oscillatory peptidization of l-proline (l-Pro). Our earlier studies have been focused on the two sulfur-containing proteinogenic α-amino acids, i.e., l-cysteine (l-Cys) and l-methionine (l-Met), and it seemed interesting to assess the effect induced by D2O on one more proteinogenic α-amino acid, i.e., l-Pro. It needs to be added that unlike l-Met, but similar to l-Cys, the oscillatory peptidization of l-Pro dissolved in the organic-aqueous solvent characterizes with the circadian rhythm. As analytical techniques, we used high-performance liquid chromatography with the evaporative light-scattering detection (HPLC-ELSD), mass spectrometry (MS), scanning electron microscopy (SEM), and turbidimetry. The obtained results can in certain sense be viewed as analogous to those earlier reported for l-Cys and l-Met by demonstrating that heavy water considerably hampers the oscillatory peptidization of l-Pro. However, an unexpected observation was also made than unlike the cases with l-Cys and l-Met, the observed hampering effect of D2O on the oscillatory peptidization of l-Pro is not monotonously dependent on the concentration of D2O in the system, but it is the strongest pronounced for 10% (v/v) D2O in the employed binary methanol–water solvent (with the investigated proportions of D2O in this solvent changing from 0 to 30%). Although we have no rational explanation for this striking effect, we believe that it should not pass unnoticed and therefore it is emphasized in this study. Maybe this firm quantitative result will prove an inspiration for future researchers interested in getting a deeper insight into the role of D2O in life processes, and more specifically in the kinetic and the mechanistic aspects thereof.