Spain is the second largest European producer of oranges and the fourth in the world. Moreover, in Andalusia, the land dedicated to organic farming of oranges has doubled in the last decade (2006–2016). The great challenge in the organic farming sector is to find a reliable analytical technique (or a set thereof) to verify that the method of production followed the organic production guidelines. A new methodology based on stable isotopes, (poly)phenol profiling and conventional quality data in the edible and non-edible parts of the oranges was developed using data fusion techniques. This system allowed authenticating organic fresh oranges. The application of a low level data fusion and a non-linear algorithm (k-nearest neighbors), obtained 100% specificity and sensitivity in the test set models. This work presented a new focus on dealing with the problem of the authentication of fruits grown under organic farming techniques.