Limonin can be effectively degraded by Rhodococcus fascians cells. These bacteria can be entrapped in K-carrageenan, and used in a continuous stirred tank reactor to degrade limonin in a continuous process. The effects of temperature, limonin concentration, dilution rate, and aeration on the reactor behaviour have been tested, and the results correlated with changes in limonin conversion, substrate degradation rate, and free and immobilized biomass. Results showed that the immobilized cells were able to debitter limonin-containing media and the immobilized biomass was quite stable throughout the operational conditions tested. A population of free biomass was present in the reactor, the quantity of which was dependent on dilution rate. The immobilized bacteria increased its limonin-degrading capability when the substrate concentration was increased. The aeration was not strictly necessary for limonin degradation. Additionally, the immobilized cells were active and stable for more than 2 months of continuous operation, and were able to recover their limonin-degrading capability when used intermittently. Finally, none of the main components of a juice was noticeably altered during limonin degradation, so the reactor response was good enough to consider its application.