This study quantifies phenolic and flavonoid compounds and evaluates the antioxidant activity by the DPPH (2,2-diphenyl-1-picrylhydrazyl) method, also identifying some secondary metabolites of R. sativus under organic fertilization and water stress. For this, a greenhouse experiment was carried out with the preparation of plant extracts (leaves and roots), quantification of phenolic and flavonoid compounds, analysis of antioxidant activity, and phytochemical screening. Different classes of secondary metabolites (catechins, steroids, saponins, among others) were identified. The DPPH method showed that the leaf extract has higher DPPH radical scavenging activity. The leaf extract had a high content of phenolic compounds, especially in treatments without water stress, either with organic fertilization (1925.59 mg GAE/g extract) or with mineral fertilization (2058.47 mg GAE/g extract). For root extracts, R. sativus developed under water stress and organic fertilization showed higher phenolic content (1383.24 mg GAE/g extract). Regarding flavonoid content, the root extract that showed the highest concentration corresponded to the treatment under water stress and without fertilization (82.1 mg QE/g extract). Therefore, radish was shown to be rich in bioactive compounds and with antioxidant potential in both its leaves and roots.