The effect of pH on iron-containing complex coacervate core micelles [Fe(III)–C3Ms] is investigated in this paper. The Fe(III)–C3Ms are formed by mixing cationic poly(N-methyl-2-vinylpyridinium iodide)-b-poly(ethylene oxide) [P2MVP41-b-PEO205] and anionic iron coordination polymers [Fe(III)–L2EO4] at stoichiometric charge ratio. Light scattering and Cryo-TEM have been performed to study the variations of hydrodynamic radius and core structure with changing pH. The hydrodynamic radius of Fe(III)–C3Ms is determined mainly by the corona and does not change very much in a broad pH range. However, Cryo-TEM pictures and magnetic relaxation measurements indicate that the structure of the micellar cores changes upon changing the pH, with a more crystalline, elongated shape and lower relaxivity at high pH. We attribute this to the formation of mixed iron complexes in the core, involving both the bis-ligand and hydroxide ions. These complexes are stabilized toward precipitation by the diblock copolymer.