Crystalline calcium carbonates (CCCs) are among the most widespread minerals on the Earth’s surface and play a crucial role in the global carbon cycle, heavy metal sorption and incorporation. Among the numerous factors that influence the precipitation of CCCs from solution, the most determinant are the presence of additives in the mineral-forming medium, temperature, and crystallization time (aging time). The current work fills the gaps in the study of calcium carbonate crystallization from heavy metal (Me2+ = Co, Ni, Cu Fe)-containing solutions (Me2+/Ca 0.005–1.600) at different temperatures (3 and 23 °C) and aging times (21–158 days). The resulting precipitates were studied using optical and scanning electron microscopy, powder X-ray diffraction and energy-dispersive X-ray spectroscopy. Three crystalline calcium carbonates (synthetic analogues of calcite, aragonite and monohydrocalcite), as well as amorphous carbonate (AC), were found in the resulting precipitates. Temperature and aging time have a considerable effect on the phase composition, morphology and heavy metal content in CCCs. Low temperature (3 °C) and short aging times are generally favorable for the formation of monohydrocalcite and amorphous carbonate, while calcite tends to form at a higher temperature (23 °C) and in long-term experiments. Heavy metals can be incorporated into the calcite/monohydrocalcite crystal lattice in sufficient amounts, while aragonite can host a very small amount of Me2+ (or none). Calcite can concentrate Co (up to ~0.25 atoms per formula unit (apfu)) and Ni/Cu (up to ~0.05 apfu), while its Fe content is very close to the detection limits. Calcite precipitated at a higher Me2+/Ca ratio and temperature (23 °C) contains less Me2+ compared to calcite precipitated at a lower Me2+/Ca ratio and temperature (3 °C). Monohydrocalcite can host up to ~0.1 apfu of Co/Ni/Cu with no detectable preference for Me2+. The amount of Me2+ in monohydrocalcite decreases as aging time or temperature increases. It is worth noting that AC is the main carrier of heavy metals in the system being investigated and it should be considered the main host phase in heavy metal adsorption from aqueous solutions. The results obtained can be used to solve environmental issues and in mineral resource management.