There is a growing concern about environmental pollution with digestate, which is produced in significant amounts in the anaerobic digestion process. The inappropriate application of digestate in agriculture may lead to ammonia emission to the atmosphere, nutrients infiltration to groundwater and surface waters eutrophication. There is a great interest in the development of efficient downstream technologies that will help better handle digestate. This study assessed the effect of three different disintegration methods (ozonation, ultrasonication, combination of ozonation and ultrasound) on solids content, nutrient concentration and biodegradability of the liquid fraction of sugar beet pulp digestate. The influence of initial pH (7, 8, 9), ozone dose (0.05–0.45 g O3/g TS), specific ultrasound energy (10,381–51,903 kJ/kg TS) and vibration amplitude (50, 100%) on the performance of digestate liquid fraction treatment was investigated. The highest removal efficiencies of organic substances, total and ammonia nitrogen averaging at 13.81, 20.04 and 28.70%, respectively, in separate ozonation and ultrasonication processes, was obtained at ozone dose of 0.25 g O3/g TS, specific energy of 41, 522 kJ/kg TS and amplitude of 100%. The application of combined processes, first ultrasonication and then ozonation, resulted in an increase in the above-mentioned removal efficiencies to 58.16, 36.60 and 48.71%, respectively.