The stable isotopic ratios and elemental compositions of 120 banana samples, Musa spp. (AAA Group, Cavendish Subgroup) cultivar Williams, collected from six countries (Colombia, Costa Rica, Dominica Republic, Ecuador, Panama, Peru), were determined by isotope ratio mass spectrometry and inductively coupled plasma mass spectrometry. Growing conditions like altitude, temperature, rainfall and production system (organic or conventional cultivation) were obtained from the sampling farms. Principal component analysis (PCA) revealed separation of the farms based on geographical origin and production system. The results showed a significant difference in the stable isotopic ratios (δ13C, δ15N, δ18O) and elemental compositions (Al, Ba, Cu, Fe, Mn, Mo, Ni, Rb) of the pulp and peel samples. Furthermore, δ15N was found to be a good marker for organically produced bananas. A correlation analysis was conducted to show the linkage of growing conditions and compositional attributes. The δ13C of pulp and peel were mainly negatively correlated with the rainfall, while δ18O was moderately positively (R values ~0.5) correlated with altitude and temperature. A moderate correlation was also found between temperature and elements such as Ba, Fe, Mn, Ni and Sr in the pulp and peel samples. The PCA results and correlation analysis suggested that the differences of banana compositions were combined effects of geographical factors and production systems. Ultimately, the findings contribute towards understanding the compositional differences of bananas due to different growing conditions and production systems linked to a defined origin; thereby offering a tool to support the traceability of commercial fruits.