The present work contributed to the patterns of crystallization affected by the metabolism of fungi and bacteria in various trophic conditions and specifically covers the case of Penicillium chrysogenum and P. chrysogenum with Bacillus subtilis. The cultivation of microorganisms was carried out on the dolomitic calcite marble in liquid Czapek–Dox nutrient medium with glucose concentrations of 1, 10 and 30 g/L. The study of the crystal component of mycelium formed on the marble surface was supported through powder X-ray diffraction, scanning electron microscopy and energy-dispersive X-ray spectroscopy; the quantitative content of the extracellular polymer substance (EPS) and low-molecular-weight organic acids (LMWOAs) in the medium was determined through chromatography–mass spectrometry (GC-MS). The results obtained clearly demonstrated the unique ability of the fungus P. chrysogenum to not only release organic acids (primarily oxalic), but the EPS also which significantly affected the pH of the culture liquid and, accordingly, the carbonate and oxalate crystallization. Carbonate crystallization manifested in the presence of Bacillus subtilis as well. The transition from oxalate crystallization to carbonate and vice versa could occur with a change in the species composition of the microbial community as well as with a change in the nutritional value medium. Under the conditions closest to natural conditions (glucose content of 1 g/L), through the action of P. chrysogenum, oxalate crystallization occurred, and through the action of P. chrysogenum with B. subtilis, carbonate crystallization was observed. The identified patterns can be used to reveal the role of fungi and bacteria in the oxalate–carbonate pathway.