Non-targeted metabolomics implied that Salicornia brachiata contains essential and sulphur-rich amino acids, which are recommended by the FAO. Total phenolic content of the plant extract contains reducing capacity and reactive oxygen species (ROS) scavenging activity. A high content of nutritive indicator polyunsaturated fatty acids (PUFAs; 55–64%), including linoleic acid (C18:2; 22–27%) and alpha-linolenic acid (C18:3; 29–41%), was detected under both control and stress conditions. About 38% of saturated fatty acids, including 26% palmitic acid (C16:0), was found under the control conditions, which varied under stress. About 19 different metabolites with different bioactivities have, so far, been identified. Metabolites benzyl sulphate (m/z 93.04) and flavonoid myricatin (m/z 183.14 and 532.98) are known for their aroma and nutritive supplements. Bioactive metabolites of pharmaceutical importance, such as oxomefruside (m/z 131.07; to be used in hypertension), clonidine (m/z 210.19; to treat high blood pressure, anxiety and certain pain), carmustine (m/z 212.19; anti-neoplastic in nature) and gangliosides (m/z 879.48; anti-inflammatory), were detected in the plant extract. An important dietary supplement selenocystathionine (m/z 269.09) was identified, which is used in hyper-accumulation of anti-cancer agent selenium. Moreover, metabolites with antimicrobial (sodium cefazolin; m/z 459.82), insecticidal or fungicidal activities (dichlorophene, m/z 267.10; oxydisulfoton, m/z 271.10; sulfotep, m/z 303.41 and azothoate, m/z 355.48) were also detected. Non-targeted metabolomics, antioxidants and scavenging activities revealed the nutritional potential of the plant, making it a promising functional food for dietary supplements.