Citric acid is nowadays produced by submerged fermentation of Aspergillus niger. The process yield depends on the composition of the medium, as well as on the microorganism strain. In this work, the effect of Fe+3, Zn+2, and Mn+2 on citric acid production by A. niger NRRL 2001 is presented. The culture medium composition was glucose (120 g/L) KH2PO4 (1.0 g/L); K2HPO4 (1.0 g/L), MgSO4.7H2O (0.5 g/L), (NH4)2SO4 (3.0 g/L). The ions Fe+3, Zn+2, and Mn+2 had their concentrations changed according to an experimental design. The experiments were carried out in an orbital shaker at 200 rpm and 30°C. The strain produced an extracellular polysaccharide that was also quantified. The optimum experimental condition was found using 7.0 mg/L of Fe+3 and 6.5 mg/L of Zn+2 in absence of Mn+2. No oxalic acid formation was observed using this experimental condition. Metal contents were not significant for the production of the polysaccharide. The highest production rate (2.95 g L−1 day−1) was reached after 10 days of fermentation. After this period, the productivity decreased slightly. In 20 days, the citric acid production rate (2.44 g L−1 day−1) was 82% of the highest productivity. The conversion into citric acid increased continuously, yielding 45.8% in 20 days of fermentation.