Abstract Industrial activities and increased human population have made wastewater streams not entirely amenable to conventional treatment methods. Anaerobic digestion (AD) can treat such wastewaters with the advantage of bioresource recovery. However, the presence of solids and recalcitrant compounds in most wastewater streams may affect the AD process. Thus, combining AD with advanced oxidation processes (AOPs) such as ozonolysis is necessary. Ozonolysis can improve the biodegradability of wastewater substrates or eliminate biorecalcitrant pollutants that escape the AD process. This study combined ozonolysis with AD to treat waste activated sludge (WAS) and distillery wastewater (DWW). When applied as a pre-treatment, ozonolysis caused the rigid cell walls in WAS to rupture and solubilised the extracellular polymeric substances (EPS), leading to increased biodegradability. For the DWW, ozonolysis pre-treatment reduced the biorecalcitrant aromatic compounds to simple aliphatic compounds, thereby increasing biodegradability. In the ensuing anaerobic process, the WAS pre-treatment improved TSS and COD reductions and a 230% increase in cumulative biogas production. For the DWW, the ozonolysis pre-treatment did not significantly impact COD reduction or biogas production; however, ozonolysis as a post-treatment removed the color causing biorecalcitrant melanoidins from the anaerobically digested effluent and solubilised the sludge (TSS) washed out from the AD unit. Therefore, the AD-ozonolysis process configuration depends on the substrate being treated. Ozonolysis is best applied pre-AD for WAS treatment and post-AD for DWW.