In this study, we compared the performances of three iron-containing crystalline and amorphous catalysts, that is, Fe-Zeo-A, Fe-ZSM-5, and Fe-silica, respectively, for the degradation of phenol in an aqueous solution. Catalytic activity for the degradation of phenol was assessed by heterogeneous photolysis, Fenton, and photo-Fenton oxidation. All catalysts exhibited higher activity in the photo-Fenton process. In addition, the catalyst stability was evaluated by the estimation of the iron loss and structural variations after the oxidation processes. Results revealed that Fe-silica and Fe-ZSM-5 exhibit higher catalytic activity (~100% phenol removal), while only 64% of phenol removal over Fe-Zeo-A was observed. Moreover, among all catalysts, Fe-ZSM-5 exhibited higher stability with low iron leaching, attributed to the uniform distribution of bonded Fe in the crystalline framework and narrow channels. On the contrary, amorphous Fe-silica exhibited higher iron leaching due to the presence of isolated iron species in the structure, leading to the partial involvement of a homogeneous reaction during the degradation of phenol. The structural stability of Fe-based catalysts was examined using microscopic and spectroscopic techniques.