The use of chemical herbicides induces negative impacts on the environment, animals, and human health. It also leads to the development of herbicide-resistant weeds. In this context, natural and efficacious herbicides are highly sought after. Essential oils are natural compounds with antibacterial, fungicidal, and phytotoxic properties. For this reason, we studied the post-emergence phytotoxic effect of cinnamon essential oil (cinnamon EO) from Cinnamomum cassia under greenhouse conditions, testing it against Trifolium incarnatum (T. incarnatum) and Lolium perenne (L. perenne). The content of malondialdehyde (MDA), percentage of water loss, electrolyte leakage, and the fluorescence of treated leaves by cinnamon EO were determined in order to understand the physiological and biochemical responses. In addition, transmission electron microscopy (TEM) was used to study the effect of cinnamon EO on cellular organelles in different tissues of T. incarnatum leaves. Results showed that cinnamon EO quickly induced oxidative stress in treated leaves by increasing MDA content, impacting membrane integrity and causing water loss. TEM observations confirmed the cell desiccation by cellular plasmolysis and showed an alteration of the membrane integrity and chloroplast damages. Moreover, Raman analysis confirms the disturbance of the plant metabolism by the disappearance of some scattering bands which correspond to primary metabolites. Through our finding, we confirm that cinnamon essential oil (EO) could be proposed in the future as a potential bioherbicide and a suitable source of natural phytotoxic compounds with a multisite action on weeds.