With the dramatic increase of organic banana production worldwide, it is essential to be able to monitor compliance with organic specifications. While the detection of pesticide fraud is routinely controlled by detecting pesticide residues in organic bananas, the detection of fertilizer fraud is much more complex. We compared the d13C and d15N isotopic values of green bananas from organic and conventional farms at seven sites around the world. In our whole dataset, the d15N values of banana fruits ranged between -1.25 and + 8.91‰. In all sites, d15N values of organic banana were significantly higher than conventional fruits (mean value of + 5.24‰ and + 2.342‰, respectively). Conversely, the type of fertilization did not significantly alter d13C values. Our results suggest that it is possible, upon arrival in importing countries, to differentiate bananas grown with synthetic fertilizer from those grown with organic fertilizer.