The chemical composition of propolis varies between different types, due to the specific vegetation found near the hives and the climatic and soil conditions worldwide. Green propolis is exclusive to Brazil, produced by bees, with the resin of the plant Baccharis dracunculifolia. Brown propolis is a specific variety produced mainly in Northeast Brazil from the plant Hyptis divaricata, also known as “maria miraculosa”. Dark propolis is a variety of propolis produced by bees from the resin of the plant known as Jurema Preta (Mimosa hostilis benth). In this study, the aqueous extracts of green, brown, and dark propolis were analyzed for their antioxidant capacity using ABTS, FRAP, and DPPH, and their chemical profiles were determined using paper spray mass spectrometry. Among the three extracts, green propolis had the highest content of total phenolic compounds (2741.71 ± 49.53 mg GAE. 100 g⁻¹), followed by brown propolis (1191.55 ± 36.79 mg GAE. 100 g⁻¹), and dark propolis had the lowest content (901.79 ± 27.80 mg GAE. 100 g⁻¹). The three types of propolis showed high antioxidant capacity, with green showing the highest antioxidant capacity for the three methods used. Using paper spray mass spectrometry, it was possible to suggest the presence of 116 substances, including flavonoids (56), phenylpropanoids (30), terpenes (25), carboxylic acids (1), benzoic acid derivatives (1), fatty acids (1), amino acids (1) and alkaloids (1). The compounds in the green, brown, and dark propolis extracts reinforce the bioactive potential for application in these tree extracts’ food and pharmaceutical products.