Citric acid is produced mostly through fermentation by Aspergillus niger fungi. Alongside some other fungi, plants, algae, animals, and bacteria, A. niger can switch the electron transport chain from the classical Cytochrome Pathway to the Alternative Pathway, using the Alternative Oxidase (AOX) enzyme. Besides AOX, encoded by the aoxA gene, which is ubiquitous, some Aspergillaceae strains have developed a paralogous aoxB gene. In this study, a genetically modified A. niger strain without the aoxA gene was compared to a non-GMO wild-type strain in terms of citric acid productivity, biomass productivity, and viability. Also, the study answers whether the GMO strain uses the AOX B enzyme, encoded by the aoxB, equally to the classical AOX enzyme in the case of its absence.