In general, productions of natural pigment in submerged microorganism culture were much less than that in solid-state fermentation, because the solid-state culture can provide a support carrier for the mycelium. To improve natural pigment production, the cultivation of Monascus purpureus in submerged encapsulated cell was investigated. Monascus purpureus immobilized in polyelectrolyte complex (PEC) microcapsules, which were prepared by sodium cellulose sulphate (NaCS) and poly-dimethyl-diallyl-ammonium chloride (PDMDAAC), was a good substitute for submerged cell culture because it mimicked the solid-state environment. The repeated-batch process with encapsulated cells was studied in flasks and a bubble column. The results indicated that the bubble column was more suitable for the encapsulation culture than the shaking flasks because of its good mass transfer performance and minor shear stress on cells. Owing to the protection of the microcapsule's membrane, Monascus purpureus in microcapsules increased approximately three times over that in free cell culture with negligible cell leakage to the medium. The pigment production in the bubble column finally reached 3.82 (OD500), which was two times higher than in free cell culture. In addition, the duration of each batch was shortened to 15% of that in free cell culture.