Digestate is a rich source of nutrients that can be applied in agricultural fields as fertilizer or irrigation water. However, most of the research about application of digestate have focused on its agronomic properties and neglected the potential harm of the presence of contaminants of emerging concern (CECs). Aadvanced oxidation processes (AOPs) have proved to be effective for removing these compounds from drinking water, yet there are some constrains to treat wastewater and digestate mainly due to their complex matrix. In this study, the feasibility to remove different CECs from digestate using O₃ and O₃/H₂O₂ was assessed, and the general effect of the matrix in the oxidation was explained. While the lab-scale ozonation provided an ozone dose of 1.49 mg O₃/mg DOC in 5 h treatment, almost all the compounds were removed at a lower ozone dose of maximum 0.48 mg O₃/mg DOC; only ibuprofen required a higher dose of 1.1 mg O₃/mg DOC to be oxidized. The digestate matrix slowed down the kinetic ozonation rate to approximately 1% compared to the removal rate in demineralized water. The combined treatment (O₃/H₂O₂) showed the additional contribution of H₂O₂ by decreasing the ozone demand by 59–75% for all the compounds. The acute toxicity of the digestate, measured by the inhibition of Vibrio fisheries luminescence, decreased by 18.1% during 5 h ozonation, and by 34% during 5 h O₃/H₂O₂ treatment. Despite the high ozone consumption, the ozone dose (mg O₃/mg DOC) required to remove all CECs from digestate supernatant was in the range or lower than what has been reported for other (waste-)water matrix, implying that ozonation can be considered as a post-AD treatment to produce cleaner stream for agricultural purposes.