The ability of commercially-available citric, oxalic and gluconic acids to bind Co2+ and Zn2+ was investigated and compared with culture filtrates from Aspergillus niger, a fungus capable of citric, gluconic and oxalic acid production, grown in the presence and absence of cobalt or zinc phosphate. This work demonstrated that citric and oxalic acid and the A. niger culture filtrates can bind Co2+ and Zn2+ and in some cases, the culture filtrates were more efficient than commercial organic acids. Gluconic acid did not bind Co2+ or Zn2+ under the conditions used in this study. The presence of insoluble metal phosphates in the growth medium was found to markedly influence the production of organic acids and, while large concentrations of gluconic acid were produced in the presence of Co3(PO4)2, the culture filtrate was unable to bind Zn2+. The production of oxalic acid by A. niger when grown in the presence of Zn3(PO4)2 led to the precipitation of insoluble zinc oxalate, a phenomenon with implications for metal tolerance and toxicity. The significance of these findings in relation to the environmental mobility of metals and phosphate, and the role of fungi in such transformations are discussed.