Salinity is one of the important environmental risks affecting agricultural production in the world. Under this condition and with the conventional cultivation methods, glycophyte plants, like tomato, are subjected to many stresses, such as ion toxicity, osmotic stress, nutritional disturbance, oxidative damage and metabolic disorders, which cause growth inhibition and yield reduction. In this context, the main objective of our study was to compare the physiological, hormonal, metabolic and agronomic responses of tomato plants (Solanum lycopersicum L.) grown in monoculture (TM) or intercropping (TH) with the halophytic species Arthrocaulon macrostachyum in a salt affected soil. The results showed that the intercropping system (TH) reduced the soil electrical conductivity, and Na+ and Cl- contents, improving mineral nutrition in tomato plants compared to TM. In addition, TH decreased the osmotic stress, improved water potential and increased water use efficiency in tomato plants, whereas the integrity of gas exchange parameters were maintained; as a consequence, an increase in tomato yield was achieved. Moreover, the ratio of stress hormones (ABA, SA and JA) to growth regulating hormones (GA, auxins and cytokinins) decreased under TH. Metabolomic analysis showed clear defined patterns of differentially accumulated metabolites. Some of the metabolites with higher abundance in TH were linked to phenylpropanoid biosynthesis and phenylalanine metabolism, whereas alanine, aspartate and glutamate metabolism, monoterpenoid biosynthesis and butanoate metabolism pathways were downregulated. Our results support the importance of A. macrostachyum in the desalination of salt-affected soils and in the improvement of tomato yield in mixed culture. Indeed, this intercropping system offers farmers a low-cost biosolution that improves yields while respecting the environment.