Salicornia ramosissima J.Woods is an edible halophyte, widely distributed in the Portuguese salt marsh that has been under valorized. The aim of this study is to expand the knowledge regarding S. ramosissima bioactive composition and safety, highlighting its potential use as nutraceutical ingredient. Therefore, extracts obtained by conventional (CE) and microwave-assisted extraction (MAE) were characterized regarding phenolic profile, antioxidant activity, radical scavenging capacity and intestinal cell effects. Moreover, organic pesticides were screened to guarantee the consumers safety. The highest phenolic and flavonoid contents were observed for the CE, as well as the scavenging capacity of O2•− (IC50 = 979.36 µg/mL) and HOCl (IC50 = 90.28 µg/mL). In contrast, the best antioxidant and antiradical activities were achieved by MAE (65.56 µmol FSE/g dw and 17.74 µg AAE/g dw for FRAP and ABTS assays, respectively). The phenolic composition was similar for both extracts, being characterized by the presence of phenolic acids, flavonols, flavanols, flavones and flavanones. The predominant compound for both extracts was myricetin. None of the extracts were cytotoxic in intestinal cell lines. Vestigial levels of β-endosulfan and p,p’-DDE were identified in MAE. These results support that S. ramosissima could be a source of bioactive compounds for nutraceutic industry.