Management of digestate from manure co-digestion with a very high chemical oxygen demand (COD) to nitrogen ratio and high nitrogen loads are a major bottleneck in the development of agricultural biogas plants. The liquid phase of digestate mixed with municipal wastewater was treated in aerobic granular sludge batch reactors at cycle lengths (t) of 6 h (GSBR6h), 8 h (GSBR8h), and 12 h (GSBR12h), corresponding to nitrogen loads of 1.6, 1.2, and 0.8 g/(L·d). Thauera sp., Lacibacter sp., Thermanaerothrix sp., and Planctomyces sp. predominated in granules favoring effective granule formation and nitrogen removal. Increasing cycle lengths (t) significantly decreased proteins in soluble fraction of extracellular polymeric substances (EPS) in granules and increased polysaccharides in tightly bound EPS that resulted in higher granule diameters and higher COD removal. In GSBR6h, heterotrophic nitrification/denitrification was very efficient, but ammonium was fully oxidized in the last hour of the cycle. So in further studies, the effluent from GSBR8h was subjected to ultrafiltration (UF) at transmembrane pressures (TMPs) of 0.3, 0.4, and 0.5 MPa. A GSBR8h-UF system (TMP of 0.4 MPa) ensured full removal of total Kjeldahl nitrogen (TKN), suspended solids, and substantial reduction of COD and color with good permeate flux. The NOx-rich (about 250 mg/L), clear permeate can be reused in line with assumptions of modern circular economy.