This study investigated the plant uptake efficiency of hydrophobic versus hydrophilic nanoparticles (NPs). Surprisingly, hydrophobic oleylamine-coated Cu₂ₓSe NPs (CS@OA) showed ~1.3 times greater uptake efficiency in tomato plants than hydrophilic chitosan-coated Cu₂ₓSe NPs (CS@CH). Atomic force microscopy (AFM) revealed that hydrophobic NPs exhibit non-spontaneous but energetically favorable root trapping and penetration. Differences in NP translocation from roots to shoots were observed and correlated with changes in the protein corona, as identified by 2D-PAGE analysis. Toxicity assays indicated insignificant toxicity at the given concentration. This research suggests potential applications in fertilizer delivery.