The metabolic profile of the brown macroalga Sargassum cymosum was analyzed after 7 days of laboratory cultivation in three salinities (30, 35, and 40 psu) and four irradiation treatments for 3 h per day: PAR-only (control; 70 μmol photons m−2 s−1), PAR+UVA (0.70 W m−2), PAR+UVB (0.35 W m−2), and PAR+UVA+UVB. Carbon (C) and nitrogen (N) levels, protein content, free polyamines (PAs), carbohydrates, phenolics, and enzymatic activities of NADH dehydrogenase and complex II were analyzed. Treatments showed variations in CN levels, with a significant reduction of C, but no evident trend for N, probably as a result of C-N balance allocation for basic biological maintenance and stress defense metabolism. Three different PAs were detected, including putrescine (PUT), spermidine (SPD), and spermine (SPM), and their variation could be explained by a defense mechanism in which PAs bound to phenolic compounds migrate through the cell wall and then degrade, concurrent with the photoprotective degradation of chlorophyll. Metabolic profiles detected through attenuated total reflection Fourier transform infrared spectroscopy/principal component analysis (ATR-FTIR/PCA) mostly showed differences in the metabolism of proteins and phenolics. It can be concluded that S. cymosum is less affected by salinity than exposure to ultraviolet radiation (UVR). Further studies are required to better understand the variation in PAs under resistance to stress. In addition to its exploitation as a complementary compound in fertilizer, it is suggested that S. cymosum could also be studied as a natural product for its antioxidant properties and high presence of phenolics and PAs, in addition to its use in nutraceutical products, human food, and animal feed.