The Melipona subnitida bee (commonly known as jandaíra) is endemic to the Caatinga biome in northeastern Brazil. This species produces a combination of beeswax, plant resins, pollens, and earth known as geopropolis to seal beehives. Thirty samples of geopropolis from M. subnitida were collected in meliponaries from 10 different locations of the semiarid region in the Rio Grande do Norte state (northeastern Brazil). Samples were subjected to palynological analysis, solid phase extraction, total phenolic content, radical scavenging activity, and ultra-performance liquid chromatography coupled with a diode array detector and quadrupole time-of-flight mass spectrometry (UPLC-DAD-qTOF-MS/MS) analyses. Palynological analysis revealed that pollen from the Fabaceae family was the most abundant in the geopropolis samples, with Mimosa tenuiflora (known as jurema preta) being 90% more frequent than other pollen types. The UPLC-DAD-qTOF-MS/MS analysis showed two distinct phenolic profiles: profile 1 had a combination of galloyl hexosides, ellagic acid, acyl-(cinnamoyl/coumaroyl)-hexosides, acyl-(cinnamoyl/coumaroyl)-galloyl-hexosides, and acylated-O-glycosides, and profile 2 had aglycone-type flavonoids. Three samples had mixed compounds from both profiles. Geopropolis samples from profile 1 had high total polyphenolic content correlated with radical scavenging activity (suggesting antioxidant capacity), while those from profile 2 had identical compounds to the apices and flowers of jurema preta, both rich in flavonoid aglycones. Principal component and hierarchical cluster analyses characterized the chemical composition of samples and identified patterns of similarity and variation. The chemical diversity observed in geopropolis samples of M. subnitida from different regions of the Caatinga suggested promising applications in food, pharmaceutical, and cosmetic industries, justifying further investigation.