The membrane bioreactor (MBR) used in this study consisted of a jet loop bioreactor (aerobic high rate system) and a membrane separation unit (microfiltration). Jet loop membrane bioreactor (JLMBR) system is a high performance treatment system. High organic loading rates can be achieved with a very small footprint. The JLMBR is a compact biological treatment system which requires much smaller tank volumes than conventional activated sludge system. Solid–liquid separation is performed with a membrane. The JLMBR system, of 35 L capacity, was operated continuously for 3 months with a sludge age of 1.1–2.8 days and chemical oxygen demand (COD) loads of 3.5–33.5 kg COD m −3 day −1. The mean concentration values of COD, total nitrogen (TN) and PO 4 3− in cheese whey (CW) were found as 78,680 mg L −1, 1125 mg L −1 and 378 mg L −1, respectively. Ninety-seven percent COD removal rate was obtained at the sludge age ( Θ c) of 1.6 days and volumetric loads of 22.2 kg COD m −3 day −1. TN removal was obtained as 99% at the loading rates of 17–436 g TN m −3 day −1. PO 4 3− removals were between 65 and 88% for the loading of 30–134 g PO 4 3− m −3 day −1. The system could simultaneously remove the COD, TN and PO 4 3− at high efficiencies. The sludge flocks were highly motile, dispersed and had poor settling properties.