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At appropriate concentrations, selenium (Se) is beneficial for humans. Tomato appears to be one of the best commodities for producing Se-biofortified fruit for dietary supplementation. To assess the efficacy of different enrichment protocols, a total of four on-plant and off-plant trials were conducted. Hydroponically grown tomato plants were sprayed with: (i) chemically synthesized Se nanoparticles (SeNPs) at 0, 1, and 1.5 mg Se L⁻¹ at blooming; (ii) sodium selenate (Na₂SeO₄) or SeNPs solution at 0, 5, and 10 mg Se L⁻¹ when the fruit entered the immature green stage. With regard to the off-plant trials, harvested mature green fruit were immersed in Na₂SeO₄ solution: (iii) at 0, 5, 10, and 20 mg Se L⁻¹ for 15 s under a vacuum; (iv) at 0, 40, and 80 mg Se L⁻¹ for 1 h. Spraying Na₂SeO₄ induced higher Se accumulation in plant tissue than SeNPs: both protocols were effective in enriching tomatoes. Postharvest Se enrichment via vacuum infiltration caused textural damage, whereas passive immersion in solution induced fruit Se accumulation without causing any damage. SeNPs appear to be quantitatively less effective than Na₂SeO₄, but might be environmentally safer. Elemental Se carried by NPs may be more easily incorporated into organic forms, which are more bioavailable for humans. Passive immersion may represent an alternative Se-enrichment strategy, allowing for the biofortification of harvested tomato fruit directly, with lower risks of environmental pollution.