Geochemical proxies of carbonates are widely applied in Quaternary paleoclimate reconstructions. However, differences in formation processes among secondary carbonate types can yield divergent environmental signals, making their reconstructions not directly comparable. Here, we compare the S13C and S18O values of two types of secondary carbonates from the Mangshan loess-paleosol section on the southeastern margin of the Chinese Loess Plateau: non-biogenic carbonates (bulk, clay-sized samples and nodules) and biogenic carbonates (fossil land snail shells), to evaluate their consistency and identify the causes of discrepancies. Fossil snail shells exhibit only minor aragonite-to-calcite transformation (average calcite content 5.4%), whereas non-biogenic carbonates consist of secondary calcite without detrital dolomite. The S13C values of land snail shells vary from-6.87 %o to-1.59 %o, lower than those of bulk samples (from-3.57 %o to-1.51 %o), clay-sized samples (from-5.12 %o to-1.27 %o), and nodules (from-3.46 %o to-1.56 %o). These isotopic offsets are also observed in modern samples and other sections, mainly reflecting differences in plant types recorded by the two carbonate types, along with a minor contribution from atmospheric CO2. By contrast, the S18O values of shells (-9.61 %o to-2.83 %o) are higher than those of bulk samples (-9.88 %o to-8.77 %o), clay-sized samples (-10.34 %o to-7.61 %o), and nodules (-9.92 %o to-9.10 %o). This suggests that stronger evaporative enrichment occurred in surface soil water for snail shell formation, compared with subsurface soil water involved in pedogenic carbonate formation. Overall, the geochemical differences between biogenic and non-biogenic carbonates arise from distinct formation processes; therefore, using those geochemical proxies for paleoclimate reconstruction needs caution.