Poor germination and seedlings growth can lead to significant economic losses for farmers, therefore, sustainable agricultural strategies to improve germination and early growth of crops are urgently needed. The objective of this work was to evaluate selenium nanoparticles (Se NPs) as nanopriming agents for tomato (Solanum lycopersicum) seeds germinated without stress conditions in both trays and Petri dishes. Germination quality, seedlings growth, synergism-antagonism of Se with other elements, and fate of Se NPs, were determined as function of different Se NPs concentrations (1, 10 and 50 ppm). Results indicated that the germination rate in Petri dishes improved with 10 ppm, while germination trays presented the best results at 1 ppm, increasing by 10 and 32.5%, respectively. Therefore, seedlings growth was measured only in germination trays. Proline content decreased up to 22.19% with 10 ppm, while for same treatment, the total antioxidant capacity (TAC) and total chlorophyll content increased up to 38.97% and 21.28%, respectively. Antagonisms between Se with Mg, K, Mn, Zn, Fe, Cu and Mo in the seed were confirmed. In the case of seedlings, the N content decreased as the Se content increased. Transmission Electron Microscopy (TEM) imaging confirmed that Se NPs surrounded the plastids of the seed cells. By this finding, it can be inferred that Se NPs can reach the embryo, which is supported by the antagonism of Se with important nutrients involved in embryogenesis, such as K, Mg and Fe, and resulted in a better germination quality. Moreover, the positive effect of Se NPs on total chlorophyll and TAC, and the negative correlation with proline content with Se content in the seed, can be explained by Se NPs interactions with proplastids and other organelles within the cells, resulting with the highest length and fresh weight when seeds were exposed to 1 ppm.