The Cu/Co-alpha-NiMoO4 nanorods were fabricated by microwave hydrothermal process and characterized by various techniques. According to XRD/HRTEM/SAED/EDS analysis, the dopant ions were existed in the lattice of alpha-NiMoO4. The Cu/Co-alpha-NiMoO4 samples have capacity to inactivate the multidrug resistant Pseudomonas aeruginosa in visible light within 180 min. Also, they revealed the excellent stability with reusability. The scavengers test indicates that H2O2/OH center dot/O-2 (center dot-) /h(+) play a crucial work for pathogen inactivation. Also, NBT assay suggested the enhancement of intracellular O-2 (center dot-) production in Cu (33 folds) and Co doped (29 folds) alpha-NiMoO4. The FESEM analysis revealed dead bacteria cells by attack of active species on cell wall. Also, DNA fragmentation (gel electrophoresis) and protein degradation (Bradford assay) confirmed the inactivation of bacteria by active species. The evidence of superior biofilm penetration ability (69%) by doped photocatalyst was exhibited by well plate based crystal violet assay and TEM/EDS mapping. The band gap reduction, surface plasmon resonance effect, oxygen vacancy, electron-hole trapping by Cu2+ /Co2+ /Co3+, formation of intermediate energy band, and efficient separation of electron-hole pair were contributed for enhancement of the pathogen inactivation in visible light by doping of Cu and Co in alpha-NiMoO4. Also, Cu doped photocatalyst has slightly more pathogen inactivation efficacy than Co doped photocatalyst. The toxicity of photocatalyst was evaluated by using RAW 264.7 cells via MTT assay and the result revealed the toxicity. In conclusion, the Cu/Co-alpha-NiMoO4 photocatalyst can be applied for efficient inactivation of multidrug resistant pathogen in biological waste water treatment.