Microfungi were able to alternate solid substrate in various environments and play a noticeable role in the formation of insoluble calcium oxalate crystals in subaerial biofilms on rock surfaces. The present work describes how iron oxalate dihydrate humboldtine is acquired under the influence of the acid-producing microscopic fungus Aspergillus niger on the surface of two iron-bearing mineral substrates in vitro. Pyrrhotite and siderite rocks, as well as the products of their alteration, were investigated using a complex of analytical methods, including powder X-ray diffraction, optical microscopy, scanning electron microscopy and EDX spectroscopy. The effect of the underlying rocks with different composition and solubility and different oxidation states of iron on Fe-oxalate crystallization and on the morphology of humboldtine crystals was shown. The mechanisms of humboldtine formation were discussed. The results obtained in vitro seem promising for using fungi in bioleaching iron and other metals from processed ores and for the development of environmentally friendly biotechnologies.