The search for more effective methods to alleviate the negative effects of exogenous stresses in plants has inspired nanotechnologies. 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 phytocouriers. 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.