Membrane filtration of biological suspensions is frequently limited by fouling. This mechanism is well understood for ultrafiltration of activated sludge in membrane bioreactors. A rather young application of ultrafiltration is the recovery of nutrients from anaerobic digestates, e.g., from agricultural biogas plants. A process chain of solid/liquid separation, ultrafiltration, and reverse osmoses separates the digestate into different products: an organic N-P-fertilizer (solid digestate), a recirculate (UF retentate), a liquid N-K-fertilizer (RO retentate) and water. Despite the preceding particle removal, high crossflow velocities are required in the ultrafiltration step to overcome fouling. This leads to high operation costs of the ultrafiltration step and often limits the economical application of the complete process chain. In this study, under-stoichiometric ozone treatment of the ultrafiltration feed stream is investigated. Ozone treatment reduced the biopolymer concentration and apparent viscosity of different digestate centrates. Permeabilities of centrate treated with ozone were higher than without ozone treatment. In a laboratory test rig and in a pilot plant operated at the site of two full scale biogas plants, ultrafiltration flux could be improved by 50–80% by ozonation. Nutrient concentrations in the fertilizer products were not affected by ozone treatment.