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In recent decades, the concept of pedogenic carbonates as a paleoenvironmental record and consequently as an instrument for paleoenvironmental reconstruction has become an increasingly high-priority research area. Especially popular are paleoenvironmental reconstructions based on the stable isotope signature of pedogenic carbonates. However, despite the exponential increase in the number of studies, the variety of carbonate morphologies as well as the overall complexity of the soil carbonate record are not sufficiently considered in the analysis of stable isotopes and dating. Examples of soils with calcic horizons in drylands with similar annual precipitation sums, but differ in their temperature regimes: Chihuahuan and Mojave Deserts (sites under investigation correspond to BWk, cold desert climate in the Koppen-Geiger system), and cold short grass steppes of South Siberia, Russia (Dwc, Monsoon-influenced subarctic climate) will be reviewed concerning their morphological and micromorphological variety, isotopic composition, and radiocarbon ages of their carbonates to support the idea of the complexity of the soil carbonate record. Polygenetic, polymorph, and polychronous pools of carbonates will be examined in these soils, highlighting the challenges and hidden dangers in the interpretations of their record. Taking into account the high heterogeneity of soil carbonates, especially those in mature soils (various morphologies including lithogenic, different generations of in situ, and ex-situ pedogenic carbonates) and the whole complexity of soil inorganic carbon (SIC) memory, data on content, composition (Ca/Mg ratio), isotope signatures (C, O, Sr, Ca, etc.), and numerical dating of carbonates in soils derived from bulk samples are often too aggregated for reliable paleoenvironmental interpretations. Diversified studies of SIC pools with special attention to their origin, morphologies, and generations—combining micromorphological techniques with nondestructive elemental (micro-XRF), isotopic studies (NanoSIMS), and numerical chronology studies after micro-contextual subsampling—are among the most promising pathways for progress in better understanding the memory of soil carbonates.