The present study emphasizes on the effect of immobilization on the decolorization of malachite green using Pseudomonas putida. The bacteria were immobilized using calcium alginate entrapment method. The effect of pH, temperature, dye concentration, inoculum volume was studied using One Factor At a Time approach for the decolorization of malachite green using calcium alginate immobilized Pseudomonas putida. Malachite green was decolorized by around 97% with the immobilized bacterium and the optimal conditions were found to be pH 7, 30°C temperature, 200 mg/L dye concentration and 6 immobilized beads. The degree of decolorization using immobilized Pseudomonas putida cells was found to be higher than free Pseudomonas putida cells. The immobilized beads were fed into a packed bed reactor and used to treat malachite green batchwise. The use of the reactor to decolorize dye improved its scope for large scale decolorization of textile effluents. Thus the use of immobilized Pseudomonas putida in the decolorization of dyes is an environmental friendly method which offers many advantages like reusability, low cost product formation, enhanced thermal and chemical stability, lesser downstream processing steps and ease of handling.