Idiophase, the citric acid producing stage of Aspergillus niger was mathematically modeled to identify required genetic manipulations to optimize citric acid production rate. For this reason, a consistent picture of cell functioning had to be achieved. The transient idiophase nature was established by stoichiometric analysis. The main intracellular fluxes were computed by application of material and physiological constraints (ATP, reduction equivalents, proton motive force) at culture time 120 hours. The HMP pathway accounts for 16% of the glucose input (carbon basis), the Krebs cycle for 13% and the citric acid synthesis for the remaining 71%. This profile implies an operative glycerol-P shuttle. It recycles 93% of the cytosolic glycerol-P to cytosolic DHAP thus coupling the transformation of cytosolic NADH to mitochondrial FADH. A cellular maintenance energy of 3.7 mmol ATP/g·h was determined. It would be spent in fueling cytoplasmatic (1.4 mmol H⁺/g·h) and mitochondrial (1.8 mmol H⁺/g·h) H⁺-ATPase pumps with efficiencies of 0.65 and 1.2 mmol H⁺/mmol ATP respectively. The role and extent of the alternative respiration system activity and polyol excretion is accounted by the model as well. In addition, the significance of GABA shunt and futile NH₄⁺/NH₃ cycle were rejected. According to the developed model, the specific citric productivity would be increased in 45% by an unique change if glucose influx were duplicated. Differences with predictions from other model that required many manipulations are also discussed.