This paper examines the impacts of fungal morphology and the yield of citric acid by Aspergillus niger and itaconic acid by Aspergillus terreus under the influence of manganese ion (Mn2+) contamination. The study indicates that the presence of manganese ions at concentrations above critical threshold can interfere with the fungal morphology and organic acid production during the fermentation of citric acid by Aspergillus niger and itaconic acid by Aspergillus terreus. Below the threshold, both fungi can form a favorable pellet morphology, leading to high organic acid yields. On the other hand, excess manganese ion concentrations induces a less productive filamentous growth which lowers the yields of the organic acids. This research establishes that controlling the concentration of manganese is necessary in the production of organic acids in industries. In general, the control of Mn2+ contamination can be considered among the best approaches to reducing cost and increasing the efficiency of industrial fermentation.