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Spinel ferrites with magnetic properties have great potential for the decontamination of aqueous systems due to their ease of recycling by magnetic separation. Herein, the purpose is to enhance ZnFe2O4spinel properties in terms of magnetization and catalytic performance viaMn substitution into the crystal structure. Zn1−xMnxFe2O4(x= 0–1) nanoclusters were successfully synthesized viaan optimal hydrothermal process, in which additives (i.e., citric acid and ammonia) play key roles in inhibiting impurity phase formation viahomogenizing the distribution of metal ions and slowing down the reaction rate. At a Zn/Mn ratio of 1 : 3, the nanocluster Zn0.25Mn0.75Fe2O4(ZMF0.75) composed of nanoparticles with sizes ranging from 5 to 10 nm shows the highest saturation magnetization (Ms = 68 emu g−1, which is ∼5 times greater than that of ZnFe2O4) and the best catalytic performance, with >99% azoxystrobin (AZX) degradation in a Fenton-like system. Moreover, the findings unveiled that the balance of Zn and Fe occupation in the polyhedron centres in the spinel crystal is broken upon replacing Zn with Mn. In all probability, the Zn/Fe/Mn cross-occupation phenomenon is essential for enhancing the activity of Fe and Mn multivalent metal atoms. A plausible mechanism for the synergistic effect of multiple active sites in ZMF0.75on the formation of HO and HO2 radicals is proposed. This work proves that Mn-substituted ZnFe2O4could be an efficient heterogeneous Fenton-like catalyst for EOC decontamination in aqueous systems with ease for recycling viamagnetic separation.