AbstractAerobic degradation of methylene blue by a pure culture of Ralstonia eutropha was studied by both freely suspended cells and kissiris‐immobilized packed bed reactors. Kissiris as a cell support matrix favored the retention of the cells in the packed bed reactor during of the methylene blue biodegradation process. The biodegradation experiments showed that the kissiris‐packed bed reactor had higher performance in removal of the dyestuff for initial concentrations equal or higher than 150 mg L−1 when compared with the freely suspended cells. To evaluate the effect of mass transfer phenomena in the immobilized system, mass balance of methylene blue for a single kissiris piece was applied to derive expressions correlating the methylene blue concentration in the bulk liquid medium and inside of the bioparticle. Kinetics studies revealed a self‐inhibitory effect of methylene blue on its biodegradation at concentrations higher than 85.76 mg L−1 in the free cell and 190.1 mg L−1 for immobilized system. The mass transfer modeling indicated the protective role of the support from cells against the inhibitory role of methylene blue is related to both external and internal mass transfer limitations in the immobilized system. In the kissiris packed bed reactor, the effectiveness value was higher than unity for initial methylene blue concentration of 150 mg L−1.