Agricultural systems must improve their sustainability and productivity to meet the growing global demand for food. A cost-effective and sustainable way is the development of biostimulants from plants rich in bioactive compounds. This study aimed to test an aqueous extract from Lemna minor L. (duckweed) on tomato plants at different concentrations (LE—0.1, 0.5 and 1.0%—weight/volume, w/v). Photosystem I and II activity, linear electron flow (LEF), electrochemical gradient across the thylakoid membrane (ECSt), shoot biomass production, root phenotyping, pigment and metabolite content were studied. LE improved many of these traits, with LE 0.5% being the most effective dosage. Compared to the untreated samples, LE significantly stimulated photosystems to use light energy while reducing the amount lost as heat (PhiNPQ and NPQt) or potentially toxic to chloroplasts (PhiNO). These results were supported by the improved shoot biomass production (number of leaves and fresh and dry weight) and root traits (number of tips, surface, volume and fresh and dry weight) found for LE-treated samples compared to untreated controls. Finally, the study highlighted that LE increased pigment and flavonoid contents. In conclusion, the research indicates that this species can be an effective and eco-friendly tool to stimulate beneficial responses in tomato.