Methylibium petroleiphilum PM1, which is capable of degrading of methyl tert-butyl ether (MTBE), was immobilized in calcium alginate gel beads. Various applications were explored to increase the mechanical strength of these gel beads. The introduction of 0.3 mol/L calcium chloride into the crosslinking solution, 0.002 mol/L calcium chloride into the growth medium, and 0.2% polyethyleneimine (PEI) as chemical crosslinking agent increased the stability of the Ca-alginate gel beads under the operation conditions of the bioreactor. The degradation rates of MTBE by the immobilized cells in the bioreactor system operated in batch and continuous mode , respectively, were compared. A MTBE biodegradation rate of 5.79 mg/L·h was reached for over 400 h (50 batches), and the immobilized cells in the bioreactor removed >96% MTBE during 50 days of operation. Molecular analysis of the PM1 cells revealed that microbial growth occurred predominantly as microcolonies in the outer area of the beads during the first 20 days of operation. The results of this study show that a continuous-mode, fixed-bed bioreactor reactor coupled with PM1-immobilized cells is a promising technology for remediating MTBE-contaminated groundwater.