Cyanobacteria and microalgae are photosynthetic microorganisms that produce bioactive compounds such as carotenoids, flavonoids, and fatty acids, which are of importance to the pharmaceutical, cosmetic, food, and biofuels industries. This study aimed to investigate the bioactive potential of extracts from the microalgae Chlorella sp. (GBBB06) and the cyanobacteria Nostoc sp. (GBBB01) and Synechococcus sp. (GBBB07), collected in the Chapada das Mesas National Park, Cerrado Maranhense. Methanolic extracts of the samples were obtained to chemically characterize them using chromatographic techniques, such as thin-layer chromatography, high performance liquid chromatography coupled with a diode arrangement detector, and gas chromatography coupled to mass spectrometry. To evaluate the antioxidant capacity, DPPH• and ABTS•+ assays were performed. Were found on liquid chromatography, peaks with characteristic wavelengths of carotenoids in the sample of Chlorella sp. and those characteristic of chlorophyll in all samples. Metabolites such as fatty acids, alcohols, and nitrogen compounds were identified via gas chromatography. In the antioxidant assessment, the samples scavenged 12% (Nostoc sp.), 20% (Chlorella sp.), and 25% (Synechococcus sp.) of the radical DPPH• in extract concentrations of 0.675 mg/mL. The results for ABTS•+ radical assay showed high antioxidant potential in the samples, with scavenging of 60% (Chlorella sp.) and 70% (Synechococcus sp. and Nostoc sp.). These results demonstrated that Chlorella sp., Nostoc sp., and Synechococcus sp. are rich in bioactive secondary metabolites with antioxidant properties and potential biotechnological applications; these extracts represent an alternative for economic exploitation of the Brazilian Cerrado in a sustainable manner.