A full scale UASB reactor treating the effluent of a malting plant was operated during nearly two years. During 37 weeks of operation the reactor worked with a COD removal efficiency of 80% and a biogas production of nearly 300 m3/d with a methane content of 77%. After the start up and during these months of operation the volumetric organic load was 4 kgCOD/m3.d and the specific organic load was between 0.2–0.4 kgCOD/kgVSS.d. The sludge SMA in this period was around 0.25 kgCOD/kg VSS.d. On week 37 as a result of a problem at the industrial process the pH in the reactor dropped to a value of 4.8. After pH recovering, the reactor worked with fluctuating COD values in the exit and showed a downward trend in the COD removal efficiency. On week 81 the presence of filaments in the granules was detected. High proportion of Chloroflexi filaments were detected by FISH in the sludge. Changes in the microbial population caused by the low pH probably destabilize the reactor performance. The presence of filamentous granules in the sludge and its further growing could be encouraged by the pH drop and the low specific organic load applied to the reactor. The low specific organic load was a consequence of the high VSS content in the UASB reactor, due to the lack of purges. The length of the filaments attached to the granules grew throughout time. In order to eliminate the sludge with poor settlement properties a recycle was applied to the reactor. As a consequence, low amount of granular sludge stayed in the reactor. At the end, COD concentration in the influent reached higher values than in normal operation; at the same time a complete sludge wash out occurred. On the other hand, using the same sludge (after the recycle implementation) in a bench scale reactor the good properties of the sludge were completely recovered.