Increased urbanization detrimentally affects crop plants. Heavy metals pollution sharply threatens food security. However, greenly synthesized nanoparticles were recently proposed as growth bioregulators. To investigate the evolved mechanisms by which sulfur nanoparticles (SNPs) could improve cellular defense against manganese toxicity, the present experiment was applied on Helianthus annuus (L.) seedlings. The experimental design was based on priming of sunflower seeds for 18 h in different (12.5–200 μM) SNPs, while 100 mM manganese sulfate (MnSO4) was implemented as irrigation treatment. The 14-day-old seedlings manifested Mn noxiousness and oxidative stress indications such as increased reactive oxygen species (O2·− and H2O2) and lipid peroxidation. Manganese exposure severely lowered the activity of some antioxidant enzymes like superoxide dismutase (SOD) and catalase (CAT), while induced ascorbate peroxidase (APX), guaiacol peroxidase (POX), polyphenol oxidase (PPO), and glutathione reductase (GR) activities. An evident decline in the pool of antioxidant compounds, such as ascorbic acid (ASA), glutathione (GSH), and total flavonoids content (TFC), was attained with Mn stress. Priming with SNPs significantly stimulated CAT and SOD activities and enhanced the antioxidant compounds (ASA, TFC, and total phenolic compounds) level in Mn-stressed seedlings. Consequently, SNPs caused a significant decrease in O2·−, H2O2, and lipid peroxidation and their oxidative damage. However, a significant reduction in GSH was detected with SNPs that might be consumed and incorporated into biosynthesis of other chelating ligands. Therefore, SNPs manifested a vital role in Mn detoxification through counterbalancing oxidative damage and elevating the antioxidant defense machinery.