With the recent development of nanotechnology, magnetic nanoparticles (mNPs) have received increasing attention as potential heterogeneous Fenton catalysts in wastewater treatment applications, as an alternative to the conventional Fenton process using dissolved iron salts. Due to their superparamagnetic properties, Fe3O4 mNPs can be easily recovered and reused by applying a magnetic field. However, Fe3O4 mNPs have a marked tendency to form aggregates in water, leading to a decrease in their catalytic yield. To overcome these limitations, this work explores the catalytic activity of Fe3O4 coated with poly(acrylic acid) (Fe3O4@PAA) as stabilized Fenton heterogeneous nanocatalyst, in the degradation of C.I. Reactive Blue 19 (RB19). To maximize the catalytic potential of Fe3O4@PAA, an experimental design based on the Response Surface Methodology (RSM) has been developed to optimize the conditions of the Fenton process in terms of Fe3O4@PAA concentration (100–300 mg L−1) and H2O2 dose (100–400 mg L−1). Based on the results obtained, a novel sequential batch reactor (SBR) coupled to an external magnetic separation system has been developed, guaranteeing the complete retention of the mNPs in the system. This system allows the reuse of Fe3O4@PAA for at least 10 consecutive cycles, with a successful decolorization of RB19 after 4 h of treatment.