Magnetic core–shell Fe3O4@La–Ce composites were prepared through a rapid coprecipitation method for adsorption of phosphate and fluoride anions from aqueous solution in a single system. Fe3O4@La–Ce was characterized by scanning electron microscopy and X-ray photoelectron spectroscopy, and it could be easily separated from aqueous solution by an external magnet. The effects of solution pH and co-existing anions on phosphate and fluorine uptake by Fe3O4@La–Ce were evaluated. The adsorption process was highly pH-dependent, and the optimal condition was pH 3 for phosphate and pH 4 for fluorine ions. The mechanism may be ligand exchange, electrostatic interaction, and Lewis acid–base interaction. The results showed that the adsorption capacity at 303 K was 51.6 and 56.8 mg/g for phosphate (calculation according to P element) and fluorine, respectively. The kinetic process was better predicted by the Elovich equation and double constant equation. Phosphate adsorption isotherms were well described by the Koble Corrigan model, while fluorine adsorption isotherms were fitted better by the Freundlich model and Redlich–Peterson model. There was coordination between La or Ce from the adsorbent and O or F from the adsorbate. Thermodynamic results demonstrated that the adsorption processes of phosphate and fluorine were spontaneous and endothermic. Fe3O4@La–Ce was highly selective and efficient to remove phosphate and fluoride from solution.