Coprecipitation facilitates the incorporation of Zn into the lattice of Fe (hydr)oxide, which is a crucial mechanism causing low Zn bioavailability in widespread Zn-deficient soils. Zn isotopes are a potential indicator of the coprecipitation of Zn and Fe (hydr)oxides in soils. However, the Zn isotope fractionation caused by coprecipitation with amorphous Fe (hydr)oxides (e.g., ferrihydrite) and the impact of environmentally relevant conditions remain unknown. Here, the molecular mechanism and impact factor of Zn isotope fractionation during Zn²⁺-Fe³⁺ coprecipitation under natural soil conditions (including different pH values and initial Zn/Fe ratios) were investigated by combining isotope ratio measurements, extended X-ray absorption fine structure (EXAFS) analyses, and density functional theory (DFT) geometry optimization. The results show that aqueous Zn (Zn_aq) can be complexed on the ferrihydrite surface (Zn_ads) with positive isotope fractionation (Δ⁶⁶Zn_ads–aq = 0.42 ± 0.09 ‰) or directly incorporated into the ferrihydrite lattice with slightly negative isotope fractionation (Δ⁶⁶Zn_stru-aq = −0.08 ± 0.03 ‰). In addition, over time, the surface-complexed Zn can further transform to a layered structure on the surface but exhibits limited Zn isotope fractionation. According to Zn K-edge EXAFS, the Zn isotope fractionation of surface complexation and incorporation of Zn_aq are related to the decrease in the Zn–O bond strength in the order surface complexed Zn (R_Zn–O = 2.00 Å) > aqueous Zn (R_Zn–O = 2.08 Å) > directly incorporated Zn (R_Zn–O = 2.06–2.07 Å with slight distortion). The limited Zn isotope fractionation associated with the transformation of Zn_ads is related to the reconfiguration of Zn_ads during the nucleation of octahedral Zn layer structures. Furthermore, the primary process controlling Zn isotope fractionation is different under varying experimental conditions, leading to distinct Zn isotope fractionation between the bulk solid and solution during Zn–Fe coprecipitation. Low pH values (5.0–6.0) and initial Zn/Fe ratios (0.01–0.02) favor the direct precipitation of Zn_aq, resulting in slightly negative Zn isotope fractionation between the bulk solid and solution. In contrast, high pH values (7.0–7.5) and initial Zn/Fe ratios (0.1–0.2) favor surface complexation and the transformation of Zn_ads, leading to heavy Zn isotope enrichment in the bulk solid. These findings offer novel insights into the primary mechanism through which Fe (hydr)oxides regulate Zn bioavailability in Zn-deficient soils and provide experimental evidence supporting the potential application of Zn isotopes as an indicator for comprehending the fate of Zn controlled by Fe (hydr)oxides in soils.