Studies on the toxicity of micro- and nanomaterials in plants have primarily focused on their intrinsic effects. However, there is often oversight when considering the potential perceptual responses that plants may exhibit in response to these materials. In this investigation, we assessed the impact of three commercially available persistent luminescence materials (PLMs) that emit red, green, or blue light under various environmental conditions. We subjected rice (Oryza sativa L.), a short-day plant, to nine distinct treatments, including exposure to particles in isolation, their nocturnal afterglow, or a combination of both. We thoroughly examined rice seedling morphology, photosynthesis patterns, metabolite dynamics, and flowering gene expression to determine the biological responses of plants to these particles. These findings demonstrated that PLMs stably interact with rice, and their emitted afterglow precisely matches the perceptual bandwidth of rice photoreceptors. Notably, the nocturnal afterglow from the red and blue PLMs enhanced the vegetative growth of rice seedlings while inhibiting their reproductive development. The blue PLMs exhibited the most pronounced positive effects, while the red PLMs exhibited inhibitory effects. When exposed to a combination of red and blue PLMs, rice displays enhanced growth and development. The observed alterations in the expression patterns of genes responsible for flowering supported these effects. We concluded that PLMs influence rice growth and development due to their inherent properties and intermittent illumination during dark periods. Both factors collectively shape rice growth and development.