Discharge from Wastewater Treatment Plants (WWTPs) can result in the emission of organic micropollutants (OMPs) and microplastics (MPs) into the aquatic environment. To prevent this harmful release, a pilot plant consisting of an ozonation followed by a granular activated carbon (GAC) filter was operated at a WWTP in Germany, and its side-effects on the concentrations of nitrogen (N) and phosphorous (P) compounds were measured. Over 80% of OMPs and transformation products were removed during the operating time (around 6000 bed volumes) no matter the ozone dose (from around 0.1 to 0.5 mgO3/mgDOC), except for Diatrizoic acid, whose breakthrough appeared at 3500 BV. Formation of the oxidation by-product, NDMA, increased with higher ozone doses, but the concentration remained below 100 ng/L. Bromate was formed at a higher ozone dose (>0.4 mgO3/mgDOC) but at a low concentration—below 10 µg/L. The MP particles detected in the inflow (PE, SBR, PP, and PS) were effectively eliminated to a high degree, with a removal rate of at least 92%. Carbon parameters (COD, DOC, and SAC254) were removed further by the pilot plant, but to different extents. As expected, nitrate was formed during ozonation, while nitrite’s concentration decreased. Further, nitrite decreased and nitrate increased within the GAC filter, while ammonium was eliminated by at least 90%. Total P concentration decreased after the pilot, but the concentration of PO4-P increased.