Degradation of basic blue 3 (BB3) was studied in a pilot scale fluidized‐bed reactor (FBR) utilizing natural magnetite (NM) nanostructures for heterogeneous Fenton process. The morphology, structure, and specific surface area of NM nanostructure were determined employing scanning electron microscopy, X‐ray diffraction, X‐ray photoelectron spectroscopy (XPS), and Brunauer‐Emmett‐Teller (BET) methods, respectively. High mass transfer coefficients, continuous operating condition and high reaction rates due to suitable and sufficient contact of phases, can be noted as significant advantages of FBR. Influences of factors, which affect performance of fluidized‐bed heterogeneous Fenton process (NM/H2O2), for instances initial concentration of contaminant and H2O2, initial pH of solution and dosage of catalyst were investigated. At the desired operational condition, pH 5, 4 mM of H2O2, and 2.27 g/L of NM after 190 min, the degradation percentage of 84%. Excess amounts of catalyst dosage and hydrogen peroxide tend to scavenge hydroxyl radicals by H2O2 molecules. Whereas low initial concentration of the dye and low initial solution pH, enhanced the BB3 degradation. Reusability of NM through five successive experiments, demonstrated the acceptable proficiency of NM as catalyst for oxidative BB3 degradation. © 2017 American Institute of Chemical Engineers Environ Prog, 36: 1039–1048, 2017