Sorting of secretory cargo and retrieval of components of the biosynthetic pathway occur in organelles such as the Golgi apparatus, the endoplasmic reticulum and the endosomes. In order to perform their functions in protein sorting, these organelles require a weakly acidified lumen. In vitro data have shown that Golgi luminal pH is in part regulated by an anion channel called Golgi pH Regulator (GPHR). Mammalian cells carrying a mutated GPHR version present an increased luminal pH leading to delayed protein transport, impaired glycosylation and Golgi disorganization. Using Drosophila as a model system, we present here the first phenotypic consequences, at the organism level, of a complete lack of GPHR function. We show that, although all individuals carrying complete loss-of-function mutations in the dGPHR gene can go through embryonic development, most of them die at late larval stages. The dGPHR mutations are, however, sublethal and can therefore generate escapers that are smaller than controls. Using cellular and molecular readouts, we demonstrate that the effects of dGPHR mutation on larval growth are not due to Insulin signaling pathway impairment and can be rescued by providing dGPHR in only some of the larval tissues. We reveal that, although functionally exchangeable, the invertebrate and vertebrate GPHRs display not completely overlapping sub-cellular localization. Whereas the mammalian GPHR is a Golgi-only associated protein whose inactivation disturbs the Golgi apparatus, our data suggest that dGPHR is expressed in both the ER and the Golgi and that dGPHR mutant flies have defects in both organelles that lead to a defective secretory pathway.