Catalytic performances and leaching behavior of 9 natural iron minerals as heterogeneous electro-Fenton catalysts for the treatment of imidacloprid wastewater were studied. The results showed that magnesioferrite exhibited the best catalytic ability among these minerals with UV absorbance at 270 nm (UV270) removal of 83.59% and COD removal of 49.11% within 4 h using graphite cathode and Ti/(RuO2)0.88- (IrO2)0.12 anode at initial pH 3 with a catalyst dose of 5 g/L, a current density of 40 mA/cm2 and an electrode spacing of 2 cm. The instantaneous current efficiency (ICE) at 4 h and energy consumption (EC) reached 2.30% and 2.20 kWh/gCOD respectively. It was found that the components contained in natural iron minerals, such as Al, alkali metal (K) and alkaline earth metals (Mg, Ca, Ba), would dissolve into the electrolyte solution, raising the final pH to 6.5–8.5 and ultimately reducing the reaction efficiency. Except magnetite and magnesioferrite, other minerals, such as ilmenite and V-Ti magnetite, were likely to cause secondary pollution. The subsequent adjustment to alkaline state for chemical precipitation of leached Mn was needed. Pyrite showed relatively high leachability in hazardous elements (especially Pb), which should be carefully evaluated before its actual application in electro-Fenton process.