<p>Soil salinization is a critical threat to global agriculture, and halophytes, such as <i>Salicornia</i> spp., represent promising candidates for cultivation in saline environments. While their physiological salt tolerance has been widely studied, little is known about how salinity influences their metabolite exudation, which may mediate allelopathic interactions. In this study, we investigated the growth, nutrient balance, photosynthetic performance, and metabolomic profiles of the exudates of <i>Salicornia europaea</i> (SE) and <i>Salicornia lagascae</i> (SL) cultivated in vitro under different NaCl concentrations. Biometric and nutrient analyses showed that SL tolerated higher salinity, maintaining a stable Na⁺/K⁺ ratio and higher biomass than SE. Chlorophyll fluorescence revealed species-specific responses: SL relied on enhanced non-photochemical quenching, whereas SE additionally exhibited reduced photochemical efficiency under elevated salinity. Untargeted metabolomic profiling of root exudates (UPLC-QTOF-MS) demonstrated both common and distinct salinity-dependent patterns. Across species, amino acid metabolism (e.g., proline and branched-chain amino acids) was consistently modulated, reflecting osmoprotective functions. SL displayed broader metabolic plasticity, with induction of pathways such as monoterpenoid biosynthesis and ascorbate metabolism, associated with allelopathy and antioxidant defense. These differences suggest divergent strategies for coping with salt stress and for shaping rhizosphere interactions. Overall, our findings highlight the potential of <i>Salicornia</i> species in saline agriculture while emphasizing specific exudation profiles with ecological and agronomic implications. Moreover, this study demonstrates the utility of in vitro culture combined with metabolomics as a controlled framework for uncovering halophyte-driven allelopathic interactions.</p>