Enhancing the productivity and bioactivity of high-functional foods holds great significance. Carbon nanoparticles (CNPs) have a recognized capacity for boosting both plant growth and the efficacy of primary and secondary metabolites. Furthermore, while salinity diminishes plant growth, it concurrently amplifies the production of phytomolecules. To ensure the robust and sustainable production of nutritious food, it becomes essential to elevate biomolecule yield without compromising plant growth. Here, we assessed the CNPs priming on plant performance and metabolites of the glycophyte amaranth (Amaranthus hypochondriacus) sprouts at the threshold salinity (25 mM NaCl; i.e., salinity that does not reduce growth but enhances the metabolites of that plant). We measured growth parameters, pigment levels, and primary (carbohydrates, amino acids, organic acids, fatty acids) and secondary metabolites (phenolics, flavonoids, tocopherols). CNP priming significantly improved biomass accumulation (fresh and dry weight) and primary and secondary metabolites of amaranth sprouts. Increased photosynthetic pigments can explain these increases in photosynthesis. Enhanced photosynthesis induced carbohydrate production, providing a C source for producing bioactive primary and secondary metabolites. The priming effect of CNPs further enhanced the accumulation of essential amino acids, organic acids, unsaturated fatty acids, tocopherols, and phenolics at threshold salinity. The increase in bioactive metabolites under threshold salinity can explain the CNP priming impact on boosting the antioxidant activities (FRAP, DPPH, anti-lipid peroxidation, superoxide-anion-scavenger, hydroxyl-radical-scavenger, Fe-chelating and chain-breaking activity in aqueous and lipid phases) and antimicrobial activities against Gram-positive and Gram-negative bacteria and fungi. Overall, this study suggested that threshold salinity and CNP priming could be useful for enhancing amaranth sprouts’ growth and nutritional quality.