Stingless bees make propolis and geopropolis; the latter is characterized by the presence of small portions of soils besides the usual plant resins. These propolis are consumed by rural and indigenous communities to heal or prevent diseases and have complex chemical composition; then to get a full understanding of their chemicals it is necessary the use of complementary analytical tools. Herein the hydrophilic fraction of 50 samples of Brazilian (geo)propolis (this way referring to either propolis or geopropolis from stingless bees) was derivatised and analysed by GC-MS. Therefore, the presence of semi-volatile and non-volatile compounds belonging to chemical classes such as flavonoids, esters, terpenoids, phenolic compounds, organic acids, phenylpropanoids, fatty acids, fatty acyls, and other lipids was confirmed. Exploratory multivariate analysis indicated that bee species affects the chemical composition of (geo)propolis. It was observed that (geo)propolis from Tetragonisca angustula from the states of Paraná and São Paulo have similar chemical composition suggesting that in both regions this stingless bee have gathered similar vegetal resins to make its (geo)propolis. Alternatively, Melipona quadrifasciata and Melipona marginata have generalist collection patterns as their (geo)propolis show a variable composition depending on the geographical origin.