High-performance novel iron oxyhydroxide (limonite) nanostructure, with improved surface reactive sites, was prepared via one-pot, eco-friendly, free precursor and cold glow discharge N2-plasma technique. Natural and plasma treated (PTNL/N2) limonite samples were characterized by FESEM, XPS, XRD, FTIR, AAS, EDX, BET/BJH and pHpzc to confirm the successful synthesis. Central composite design (CCD) and artificial neural network (ANN, topology of 4:8:1) methods were utilized to study the oxidation/mineralization of phenazopyridine (PhP) as a hazardous contaminant by heterogeneous catalytic ozonation process (HCOP). The obtained results indicated that PTNL/N2 had the highest catalytic performance in PhP degradation (98.6% in 40 min) and mineralization (80.4% in 120 min). The degradation mechanism in different processes was investigated by dissolved ozone concentration, various organic scavengers (BQ and TBA) and inorganic salts (NaNO3, NaCl, Na2CO3 and NaH2PO4). Moreover, reusability-stability, Fe and nitrogen (NO3− and NH4+) ions release were assessed during different AOPs. Furthermore, toxicity tests indicated that the HCOP using PTNL/N2 was able to detoxify the PhP solutions efficiently. Finally, Density Functional Theory (DFT) studies were employed to introduce the most plausible contaminant degradation pathway, reactive sites and byproducts. This research provided a new insight into the improvement of wastewater treatment studies by a combination of experiment and computer simulation.