Wastewater from plant-based milk processing is currently being treated Sloe wastewater treatment plant (Vlissingen, the Netherlands). However, the problem occurs in the high-rate anaerobic treatment system, as the reactor is prone to biomass washout and floating layer formation. Therefore, increasing the level of sludge inside the anaerobic reactor is difficult. This study investigates the potential problems of maintaining the anaerobic granular sludge and studies what other effects the suspected components can have on the anaerobic granular sludge when converting the wastewater in the batch reactor at 35 oC. The volatile and long-chain fatty acids (VFAs and LCFAs) were fractionated to identify further the problems related to the full-scale reactor. The biochemical methane potential (BMP) test was carried out to study the relationship between the wastewater used as substrate and anaerobic granular sludge as inoculum, specifically when adding the wastewater with palmitic acid, stearic acid, and oleic acid. Results showed that there were still LCFAs, with a fraction of palmitic acid (37.78%), stearic acid (23.8%), and oleic acid (26.84%) detected in the effluent. The identified components might be strongly responsible for the problems of maintaining the level of sludge in the full-scale anaerobic reactor. However, the reactor did not suffer from the accumulation of VFAs caused by the LCFAs inhibition. Furthermore, slower conversion of soluble biodegradable COD and lower methane production occurred by adding 245 mg/L of oleic acid. Interestingly, adding 275 mg/L of palmitic acid and stearic acid caused more foam and floating layer formation in the batch reactor.