This study investigated the fluorescent properties of nanoparticles synthesized from mulberry leaf ethanolic extract using a hydrothermal method. The analysis confirmed the presence of carbon dot nanostructures exhibiting fluorescence emission peaking at 670 nm (under 405 nm excitation) with a quantum yield of 45%. Under quasi-continuous excitation at 405 nm on a silicon substrate, photobleaching of the nanoparticles was observed within 10–20 s of irradiation. In the absence of illumination, partial fluorescence recovery was detected, consisting in several percent within one minute and over 25% after 16 hours in darkness. Comparative spectral analysis of the initial leaf extract and the synthesized red-luminescent carbon dot fraction revealed similarities, suggesting the presence of unbound organic molecules with chromophoric groups in the medium. It was found that these chromophores accumulate in red blood cell membranes, enabling cell visualization; however, they exhibit both cytotoxic and phototoxic effects. Thus, the synthesis of carbon dots from multicomponent plant extracts may result in incomplete carbonization and degradation of chromophores, which can significantly influence the interpretation of the optical properties of the obtained nanostructures.