An efficient treatment process for screened cow manure waste, particularly for the degradation of natural steroid hormones, was developed. The first step in this process was a draw-and-fill process for thermophilic anaerobic digestion. After fourfold dilution with tap water, continuous feeding was performed for the aerobic treatment of the effluent from the anaerobic treatment. Batchwise ozone oxidation was then carried out for the degradation of the natural steroid hormones that remained in the effluent from the aerobic treatment. A yeast two-hybrid assay was performed to evaluate hormonal degradation. Significant reductions in the concentrations of total VFA, BOD5, CODCI, TOC, TS, VSS, and natural steroid hormones were demonstrated in the effluent from the biological treatments. The removal ratios of such concentrations were 99.7%, 90%, 79%, 84%, 51%, 58%, and 99%, respectively. Although the concentrations of the remaining TOC and CODCr remained constant, natural steroid hormones were completely removed by ozone oxidation.