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ABSTRACT Pistachio thrives in semi‐arid and arid environments and is highly adaptable to various abiotic stresses. However, soil salinization significantly threatens productivity, leading to considerable osmotic and ionic stress for these plants. Roots are the primary sites for stress perception and response; however, they remain understudied in woody crops, such asPistachio. This study examines the alterations in root protein expression and metabolic pathways in response to sodium chloride‐induced salt stress through biochemical and proteomic analyses. One‐year‐old pistachio rootstocks were treated with four different saline water regimes over a 100‐day period, and the total proteins were isolated from these samples. Over 1600 protein identifiers were detected, with comparative analysis revealing 245 proteins that were more abundant and 190 that were less abundant across three stress levels. Key pathways associated with stress tolerance, such as protein modification, folding, and heat shock protein (HSP) protection, were upregulated. An increase in secondary metabolites played a crucial role in detoxification. As salt stress intensified, the abundance of trafficking proteins increased, enhancing transporter activities. Active signaling pathways were observed at lower stress levels, while structural proteins became more critical at higher stress levels for maintaining cell membrane integrity. This cultivar exhibited enhanced kinase activities that regulate lipid and carbohydrate metabolism, thereby aiding in ion homeostasis and maintaining redox balance. The protein interaction network, mapped to orthologous proteins inArabidopsis thaliana, revealed clusters associated with cytosolic, carbohydrate, and amino acid metabolism contributing to salinity stress tolerance. The validation of proteomic data was performed by assessing corresponding changes in transcript levels. The study expands upon previous work by providing a comprehensive proteomic map of UCB‐1 pistachio rootstock across multiple salinity levels. The findings have practical implications for developing more resilient cultivars, supporting sustainable pistachio production in regions prone to salinity.