Fe(II)-catalyzed ferrihydrite (Fh) transformation is a critical process in biogeochemical cycling and contributes to paleoenvironmental reconstruction, yet the underlying mechanisms by which organic matter modulates these transformations remain poorly understood. This study elucidates how four common carboxylic ligands (acetate, oxalate, malonate and citrate), representing mono-, di- and tri-carboxylic types, regulate each step of Fe(II)-catalyzed Fh transformation, ultimately shaping transformation kinetics, and product phases. Batch transformation experiments under anoxic conditions at pH 7.0 were conducted to monitor Fe(II) speciation and intermediate labile Fe(III) (Fe(III)labile) accumulation over time, and the temporal evolution of mineral phases, morphologies, and particle sizes was investigated using powder X-ray diffraction, Fourier transform infrared spectroscopy, and transmission electron microscopy. By decoupling individual reaction step, we revealed the distinct effects of these ligands on Fe(II) adsorption on Fh, Fe(II)-Fh interfacial electron transfer (IET), and the repolymerization of Fe(III)labile into secondary minerals. The mono-carboxylic ligand acetate exhibits minimal influence on these reaction steps within the studied concentration range (0.4–2 mM). Di-carboxylic ligands (malonate and oxalate, 0.2–1 mM) reduce Fe(II) adsorption, with stronger inhibition at higher concentrations, while citrate uniquely enhances Fe(II) adsorption by forming ternary surface complexes. These results indicate that the multi-carboxylic ligands, in contrast to mono-carboxylic acetate with negligible effect, exhibit dual, concentration-dependent effects on Fe(II)-catalyzed Fh transformation: at low concentrations, they primarily enhance the electron-donating capacity of surface-associated Fe(II), thereby accelerating Fe(III)labile accumulation through promoted Fe(II)-Fh IET. As ligand concentration increases, their inhibition of Fe(III)labile repolymerization becomes dominant, markedly suppressing the consumption and nucleation of Fe(III)labile. Moreover, these inhibitory effects are more pronounced for ligands with more carboxyl groups. Notably, the strong linear correlation between effective (uncomplexed) Fe(III)labile concentrations and secondary mineral formation rates demonstrates that carboxylic ligands primarily regulate Fh transformation by modulating the availability of Fe(III)labile for nucleation, with the concept of “effective” Fe(III)labile, as refined in this study, offering a more precise mechanistic and quantitative descriptor of the reactive Fe(III) pool that remains available for nucleation despite partial complexation by carboxylic ligands. Although both are dicarboxylic ligands, malonate and oxalate differentially direct Fh transformation by altering the surface free energy and nucleation barriers of lepidocrocite and goethite through distinct adsorption structures, thus shaping their morphologies, particle sizes, and relative proportions. This study offers new mechanistic insight into how carboxylic ligands regulate Fe(II)-catalyzed Fh transformation, enhancing understanding of iron mineral-organic matter interactions and their implications for iron cycling and mineral evolution in natural environments.