The aim of this study was to characterize the individual phenolic profile and antioxidant, anti-inflammatory, cytotoxic, and antimicrobial activities of hydroethanolic and infusion extracts prepared from Algerian Saharan Juniperus phoenicea L. and Cotula cinerea (Del). The phenolic profile was determined using a liquid chromatograph coupled to a diode array detector and an electrospray ionization mass spectrometer (LC-DAD-ESI/MS). A total of thirteen and nine individual phenolic compounds were identified in J. phoenicea and C. cinerea, respectively. 3-p-Coumaroylquinic acid, quercetin- and myricetin-O-pentoside were the major compounds present in J. phoenicea; on the other hand, C. cinerea presented luteolin-7-O-glucoside, luteolin-O-malonylhexoside, and 5-O-caffeoylquinic acid as the main molecules. In general, all samples exhibited interesting antioxidant activity when compared to the standard Trolox, but J. phoenicea extracts presented the highest bioactivity. Likewise, all the samples exhibited anti-inflammatory activity; thus J. phoenicea hydroethanolic extracts showed the highest potential (88 ± 8 μg mL-1). In addition, their cytotoxicity was evaluated towards a panel of four selected cell lines (HeLa, NCI-H460, MCF-7 and HepG2), and all the extracts showed cytotoxic effects, with J. phoenicea extracts being the most effective. The in vitro antimicrobial activity of the plant extracts was moderate, Gram-positive bacteria thus being more sensitive than the Gram-negative strains (MIC values between 5 and 20 mg mL-1). The present work suggests that J. phoenicea and C. cinerea are sources of bioactive ingredients with potential use in the food and pharmaceutical industries.