The present study is focused on the effect of biofilm medium chemistry on oxalate crystallization and contributes to the study of the patterns of microbial biomineralization and the development of nature-like technologies, using the metabolism of microscopic fungi. Calcium oxalates (weddellite and whewellite in different ratios) were synthesized by chemical precipitation in a weakly acidic environment (pH = 4–6), as is typical for the stationary phase of micromycetes growth, with a ratio of Ca²⁺/C2O4²⁻ = 4.0–5.5, at room temperature. Additives, which are common for biofilms on the surface of stone in an urban environment (citric, malic, succinic and fumaric acids; and K⁺, Mg²⁺, Fe³⁺, Sr²⁺, SO4²⁺, PO4³⁺ and CO3²⁺ ions), were added to the solutions. The resulting precipitates were studied via X-ray powder diffraction (XRPD), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDXS). It was revealed that organic acids, excreted by micromicetes, and some environmental ions, as well as their combinations, significantly affect the wed-dellite/whewellite ratio and the morphology of their phases (including the appearance of tetragonal prism faces of weddellite). The strongest unique effect leading to intensive crystallization of wed-dellite was only caused by the presence of citric acid additive in the medium. Minor changes in the composition of the additive components can lead to significant changes in the wed-dellite/whewellite ratio. The effect of the combination of additives on this ratio does not obey the law of additivity. The content of weddellite in the systems containing a representative set of both organic acids and environmental ions is ~20 wt%, which is in good agreement with natural systems.