In situ Fe(III) coprecipitation from Fe2+ oxidation is a widespread phenomenon in natural environments and water treatment processes. Studies have shown the superiority of in situ Fe(III) (formed by in situ oxidation of a Fe(II) coagulant) over ex situ Fe(III) (using a Fe(III) coagulant directly) in coagulation, but the reasons remain unclear due to the uncertain nature of amorphous structures. Here, we utilized an in situ Fe(III) coagulation process, oxidizing the Fe(II) coagulant by potassium permanganate (KMnO4), to treat phosphate-containing surface water and analyzed differences between in situ and ex situ Fe(III) coagulation in phosphate removal, dissolved organic matter (DOM) removal, and floc growth. Compared to ex situ Fe(III), flocs formed by the natural oxidizing Fe2+ coagulant exhibited more effective phosphate removal. Furthermore, in situ Fe(III) formed through accelerated oxidation by KMnO4 demonstrated improved flocculation behavior and enhanced removal of specific types of DOM by forming a more stable structure while still maintaining effective phosphate removal. Fe K-edge extended X-ray absorption fine structure spectra (EXAFS) of the flocs explained their differences. A short-range ordered strengite-like structure (corner-linked PO4 tetrahedra to FeO6 octahedra) was the key to more effective phosphorus removal of in situ Fe(III) than ex situ Fe(III) and was well preserved when KMnO4 accelerated in situ Fe(III) formation. Conversely, KMnO4 significantly inhibited the edge and corner coordination between FeO6 octahedra and altered the floc-chain-forming behavior by accelerating hydrolysis, resulting in a more dispersed monomeric structure than ex situ Fe(III). This research provides an explanation for the superiority of in situ Fe(III) in phosphorus removal and highlights the importance of atomic-level structural differences between ex situ and in situ Fe(III) coprecipitates in water treatment.