Propolis samples collected from five areas in Mato Grosso do Sul state, Midwest Brazil, comprising portions of the Cerrado, Pantanal, and Atlantic Forest ecosystems, were investigated for metabolomic profiles and evaluated for antioxidant and antitumor potential. Chemical profiles were determined by HPLC-DAD-MS/MS data and evaluated using principal component analysis and hierarchical clustering analysis to discern chemical composition patterns. Based on phytogeographical origin and chemical composition, 20 potential markers were identified and five groups were distinguished: (I) Cerrado/Central, (II) Atlantic Forest/South, (III) Cerrado−Pantanal transition area/ Northwest, (IV) Cerrado/North, and (V) Pantanal/West. Drawing on HPLC-DAD-MS/MS and NMR data, 47 compounds were successfully or tentatively identified, including prenylated phenylpropanoids, flavonoids, isoflavonoids, and di-and triterpenoids, among other constituents. Isoflavonoids, typically found in red propolis from Northeast Brazil, are being reported for the first time in a propolis sample from the Midwest. A new prenylated aromatic compound, (E)-3-[4-hydroxy-3-(2-hydroxy-3methylbut-3-en-1-yl)-5-(3-methylbut-2-en-1-yl)phenyl]propenoic acid, was obtained. Samples in group II exhibited promising antitumor potential against prostate and breast carcinoma cells, as did samples in groups III and IV against the latter cell line. The sample in group I, despite containing the highest amount of total phenolic compounds and being the only sample to exhibit scavenging activity against DPPH, was not the most cytotoxic against the cell lines tested.