The search for more effective methods to alleviate the negative effects of exogenous stresses in plants has inspired nano-technologies. It is in this context that the use of formulations containing nanoporous silicon-stabilized hybrid lipid nanoparticles acting as delivery systems of the flavonoid quercetin was investigated here. These formulations, referred to as phyto-couriers, proved their efficacy in protecting the important crop model Solanum lycopersicum "Micro-Tom" against salinity. Two phyto-courier formulations, GS1 and GS3, functionalized with 25 mg of quercetin and differing in the presence of trehalose were applied to salt-stressed tomato by foliar spraying. The shape and ordered structure of the palisade cells was completely compromised under salinity; however, the phyto-couriers preserved their elongated shape under abiotic stress. From a molecular point of view, some stress-responsive genes tended to decrease in expression in stressed leaves treated with the phyto-couriers. Shotgun proteomics confirmed the nano-biostimulant nature of the formulations: several proteins involved in cytoprotection against oxidative stress were more abundant in control leaves treated with the phyto-couriers. Proteins involved in chromatin remodeling were also more abundant in control leaves treated with the trehalose-containing GS3 formulation, a finding indicating a priming effect. Overall, the formulations showed promising results to enhance abiotic stress tolerance in a crop model through the mitigation of stress symptoms. The results presented proof of the stress-relieving properties of the silicon-stabilized hybrid lipid nanoparticles and are a proof-of-concept for the use of the phyto-courier nanotechnology in horticultural applications.