The effect of the filling stage on the behavior of a mechanically stirred anaerobic sequencing batch reactor containing biomass immobilized on 1 cm polyurethane foam cubes was investigated. The reactor was made of acrylic with a capacity of 6.3 L, treating per cycle 2.5 L synthetic low-strength wastewater with a concentration of 500 mgCOD/L, at 30 ± 1°C. Eight-hour cycles (tC) and agitation of 500 rpm were utilized. At the beginning of each cycle 60% of the wastewater volume was treated, sufficient to completely cover the bed. The remaining volume was added at different fill times (tF) of 10, 120, 240, 260 and 480 min. The results obtained showed that ratios of tF/tC ≤ 0.5 enabled organic matter removal higher than 75% and 70% for filtered and non-filtered samples, respectively. Ratios of tF/tC > 0.5, despite operation stability, resulted in loss of efficiency and formation of viscous material, similar to extra-cellular polymeric substances.