The objective of this study is to investigate the consequence of ozone dosage rate on the qualitative change in organic compounds and nitrogen in anaerobic digester effluent during the ozone process. Therefore, ozonation improves the biodegradability of recalcitrant organic compounds, quickly oxidizes the unsaturated bond, and forms radicals that continue to deteriorate other organic matter. In this study, ozonation was performed in a microbubble column reactor; the use of microbubble ozone improves the status of chemical oxygen demand (COD) and changes of organic nitrogen to inorganic compounds. The ozone injection rates were 1.0, 3.2, and 6.2 mg/L/min. The samples obtained during the ozone treatments were monitored for CODMn, CODCr, TOC, NO2−-N, NO3−-N, NH4+-N, T-N, and Org-N. The ozone dose increased 1.0 to 6.2 mg/L and it increased the degradation ratio 40% and the total organic carbon 20% during 20 min of reaction time. During the ozonation, the CODCr and CODMn values were increased per unit of ozone consumption. The ozone treatment showed organic nitrogen mineralization and degradation of organic compounds with the contribution of the microbubble ozone oxidation process and is a good option for removing non-biodegradable organic compounds. The original application of the microbubble ozone process, with the degradation of organic compounds from a domestic wastewater treatment plant, was investigated.