In this paper, we report the characterization of Brazilian red propolis from two origins. The commercial value of this product is due to its composition and bioactivity, which depend on geographical factors. Total and individual phenolic, antioxidant, and medium infrared spectroscopic (MIR) characterization of 72 red propolis samples from two origins (Bahia (BA) and Rio Grande do Norte (RN), Brazil) were performed. Samples from RN showed higher concentrations of biomarkers. The BA samples showed higher antioxidant capacity despite having lower concentrations of the red propolis biomarker molecules when compared to the RN samples. The MIRS showed differences regarding the origin. The principal component analysis confirmed the differences, generating well-defined groups. Linear discriminant analysis or discriminant analysis and and partial least squares discriminant analysis showed excellent model performance. The models with MIRS data from raw propolis have a high correct classification rate and require no sample preparation. These findings can affect red propolis production, boosting sustainable extractivism, and changing the reality of small communities.