Natural chabazite (CHA) is used for the first time as a heterogeneous catalyst in Fenton-like oxidation. Pretreatment techniques (NH4+-exchange, steam treatment, and Fe-exchange) were applied to natural CHA to improve the available micropore and mesopore volume as well as to increase Fe-content. CHA samples were characterized by XRD, N2 adsorption, UV–Vis, SEM-EDX, ICP-OES, and MAS NMR to study the improvement after each pretreatment. Steam treatment at 675 °C and 20 kPa improved the mesopore volume of CHA, which enabled Fe3+ concentration to increase from 0.24 to 0.60 mmol Fe3+ g CHA−1 following the Fe-exchange. The Fe-exchanged CHA (Fe-CHA) was then tested for malathion oxidation. The effect of H2O2 and catalyst doses and pH on the degradation of malathion was investigated. Fenton-like oxidation was realized at a higher and wider pH range (pH 3–7) when compared to classical Fenton. A malathion removal between 20 and 81% was achieved depending on the initial malathion concentration (250–750 μg L−1), Fenton Reagents (H2O2 and Fe-CHA) concentrations (75–300 mg L−1 and 250–750 mg L−1, respectively) and pH (3–7). The metabolites of malathion were identified as malaoxon, desmethyl malaoxon and diethyl malate. A possible oxidation pathway was proposed, where desmethyl malaoxon and diethyl malate were identified as the secondary oxidation products. Moreover, the performance of Fe-CHA was compared with commercially available synthetic zeolites of Fe-Ultra-stable Y and Fe-ZSM-5. Fe-CHA is found to be comparably effective as these synthetic zeolites, as well as providing substantially smaller sludge production when compared to classical Fenton.