Nowadays, synthetic organic dyes and pigments discharged from numerous industries are causing unprecedentedly severe water environmental pollution, and conventional water treatment processes are hindered due to the corresponding sophisticated aromatic structures, hydrophilic nature, and high stability against light, temperature, etc. Herein, we report an efficient fabrication strategy to develop a new type of highly efficient, low-cost, and magnetically recoverable nanocatalyst, i.e., FePt–Ag nanocomposites, for the reduction of methyl orange (MO) and rhodamine B (RhB), by a facile seed deposition process. X-ray diffraction results elaborate that the as-synthesized FePt–Ag nanocomposites are pure disordered face-centered cubic phase. Transmission electron microscopy studies demonstrate that the amount of Ag seeds deposited onto the surfaces of FePt nanocrystals increases when increasing the additive amount of silver colloids. The linear correlation of the MO and RhB concentration versus reaction time catalyzed by FePt–Ag nanocatalysts is in line with pseudo-first-order kinetics. The reduction rate constants of MO and RhB increase with the increase of the amount of Ag seeds. FePt–Ag nanocomposites show good separation ability and reusability, and could be repeatedly applied for nearly complete reduction of MO and RhB for at least six successive cycles. Such cost-effective and recyclable nanocatalysts provide a new material family for use in environmental protection applications.