Present report, an investigation of highly concentrated and low bio-degradable pharmaceutical wastewater (HCPWW) treatment; simultaneously ammoniacal nitrogen recovery for struvite fertilizer. The use of multiple solvents and many formulation processes in HCPWW, resulting highly refractory chemicals. Here, in this study focused on evaluation of chemo-biocatalysts for the removal of refractory organics, nitrogen recovery from HCPWW. The initial organics, and nitrogen content in HCPWW was 20,753 ± 4606 mg/L; BOD, 6550 ± 1500 mg/L and NH4+-N, 1057.9 ± 185.8 mg/L. Initially, the biodegradability (BOD5: COD ratio from 0.32 to 0.45) of HCPWW, which was improved by heterogeneous Fenton oxidation (HFO) processes, and porous carbon (PCC, 30 g/L), along with FeSO4.7H2O, 200 mg/L and H2O2 (30% v/v), 0.4 ml/L were used as a catalyst in a weakly acidic medium. For the biocatalytic processes, the microbial culture cultivated from sewage and incorporated into a Fluidized Immobilized Carbon Catalytic Oxidation reactor (FICCO), and dominant species are Pseudomonas Putida sp., Pseudomonas Kilionesis sp., and Pseudomonas Japonica sp., which is identified by using 16 S rDNA sequencing analysis. The COD and BOD5 removal efficiency of 65–93% and 70–82%, and follow the pseudo-second-order kinetic model with the rate constants of 1.0 × 10−4 L COD−1 h−1, 1.5 × 10−3 L COD−1 h−1 and 3.0 × 10−3 L COD−1 h−1 in the HFO–FICCO-CAACO catalytic processes. The optimized hydraulic retention time (HRT) of FICCO reactor was 24 h, and 1 h for the Chemo-Autotrophic Activated Carbon Oxidation (CAACO) reactor for maximum organics removal. MAP (Magnesium Ammonium Phosphate precipitation) process showed 90% of NH4+-N elimination and recovered it as a struvite fertilizer at an optimum molar ratio of 1:1.3:1.3 (NH4+-N: Na2HPO4.2H2O: MgO). FT-IR, UV–visible, and UV-fluorescence data confirm the effective elimination of organics. Hence, this integrated treatment system is appropriate for the management of pharmaceutical wastewater especially elimination of complex organic molecules and the recovery of nitrogen in the wastewater.