The application of an anaerobic five compartment granular bed baffled reactor (GRABBR) was investigated with brewery wastewater for combined carbon and nitrate removal, with a separate downstream nitrification unit for converting ammonia to nitrate. The GRABBR was operated at an organic loading rate of 3.57 kg chemical oxygen demand (COD) m−3 d−1 and ammoniacal nitrogen (NH4-N) loading rate of 0.13 kg NH4-N m−3 d−1 when nitrified effluent from a downstream nitrification unit was recycled to the feed point of the GRABBR. Carbonaceous matter and nitrate were removed simultaneously in the GRABBR at different recycle to influent ratios (from 1 to 2), with nitrogen oxide (nitrate and nitrite nitrogen, NOx-N) loading rates varying from 0.04 to 0.05 kg NOx-N m−3 d−1. At all recycle to influent ratios, COD removal efficiency of 97% to 98% were observed in the GRABBR, and over 99% by the two-stage treatment configuration (i.e. GRABBR and nitrification unit). All the nitrates added to the GRABBR were denitrified in the first three compartments of the system. For all the recycle to influent ratios studied, almost all ammonia was converted to nitrate nitrogen with only small traces of nitrite nitrogen in the nitrification unit. Methane production was observed throughout the experimental period with its composition varying from 25% to 50%, showing that simultaneous methanogenesis and denitrification occurred. This study shows that a GRABBR could bring about a high degree of carbon and nitrate removal, with simultaneous methanogenesis and denitrification, due to plug flow granular bed multi-stage characteristics of the bioreactor.