To satisfy global food markets with continuous supply of fruits and vegetable crops during the whole season, growers in arid and semi-arid regions have increased the use of salinized water in irrigation regimes1. While plant biostimulants have been reported to be an effective solution to tackle salinity stress in different crops, the key genes and metabolic pathways involved in these tolerance processes remain unclear2-4. This study focused on integrating phenotypic, physiological, biochemical and transcriptome data obtained from different tissues of tomato plants (cv. Micro-Tom) subjected to a saline irrigation water program for 61 days (EC: 5.8 dS/m) and treated with a protein hydrolysate and Ascophyllum nodosum-derived biostimulant. The biostimulant application was associated with the overexpression of transporter genes related to ion homeostasis (e.g., HKT1;2), restricting Na+ translocation from roots to leaves and promoting K+ accumulation in roots. It allowed the maintenance of higher K+/Na+ ratios in both leaf and root tissue. A more efficient osmotic adjustment was characterized by a significant increase in RWC, which was associated with osmolyte accumulation and upregulation of genes related to aquaporins (e.g., PIP2.1). Higher content of photosynthetic pigments, increased expression of genes involved in photosynthetic efficiency and chlorophyll biosynthesis (e.g., LHC) and enhanced primary C and N metabolic mechanisms were also observed, leading to higher fruit yield and fruit number (47.5% and 32.5%, respectively). Overall, it can be concluded that this novel biostimulant can provide long-term protective effects on salinity stressed tomato plants through a well-defined mode of action in different plant tissues.