A novel Bio-Entrapped Membrane Reactor (BEMR) packed with bio-ball carriers was constructed and investigated for organics removal and membrane fouling by soluble microbial products (SMP). An objective was to evaluate the stability of the filtration process in membrane bioreactors through backwashing and chemical cleaning. The novel BEMR was compared to a conventional membrane bioreactor (CMBR) on performance, with both treating identical wastewater from a food and beverage processing plant. The new reactor has a longer sludge retention time (SRT) and lower mixed liquor suspended solids (MLSS) content than does the conventional. Three different hydraulic retention times (HRTs) of 6, 9, and 12 h were studied. The results show faster rise of the transmembrane pressure (TMP) with decreasing hydraulic retention time (HRT) in both reactors, where most significant membrane fouling was associated with high SMP (consisting of carbohydrate and protein) contents that were prevalent at the shortest HRT of 6 h. Membrane fouling was improved in the new reactor, which led to a longer membrane service period with the new reactor. Rapid membrane fouling was attributed to increased production of biomass and SMP, as in the conventional reactor. SMP of 10–100 kDa from both MBRs were predominant with more than 70% of the SMP <100 kDa. Protein was the major component of SMP rather than carbohydrate in both reactors. The new reactor sustained operation at constant permeate flux that required seven times less frequent chemical cleaning than did the conventional reactor. The new BEMR offers effective organics removal while reducing membrane fouling.