The measurement of Baryonic Acoustic Oscillations from galaxy surveys is well known to be a robust and powerful tool to constrain dark energy. This method relies on the knowledge of the size of the acoustic horizon at radiation drag derived from Cosmic Microwave Background Anisotropy measurements. In this paper we quantify the effect of non-standard initial conditions in the form of an isocurvature component on the determination of dark energy parameters from future BAO surveys. In particular, if there is an isocurvature component (at a level still allowed by present data) but it is ignored in the CMB analysis, the sound horizon and cosmological parameters determination is biased, and, as a consequence, future surveys may incorrectly suggest deviations from a cosmological constant. In order to recover an unbiased determination of the sound horizon and dark energy parameters, a component of isocurvature perturbations must be included in the model when analyzing CMB data. Fortunately, doing so does not increase parameter errors significantly.