Agarwood is the resinous product of several tree species of family Thymelaeaceae such as Aquilaria spp. Unsustainable harvesting has threatened the existence of agarwood producing species in their natural habitat. Therefore, the present study was developed to facilitate an effective and efficient method to produce Aquilaria malaccensis seedlings by In vitro culture. Here, we optimized the aeration rate in the bubble column reactor and the immersion time on the temporary immersion system (TIS)-RITA ® bioreactor and compare the growth rate of A. malaccensis with both systems. A. malaccensis shoot cultures were propagated in Murashige and Skoog (MS) semisolid medium and then pre-conditioned in thin layer culture before bioreactor cultivation. A. malaccensis shoots in the bubble column reactor were subjected to variable aeration rates of 0.05 and 0.1 vvm, while the immersion variation within the TIS-RITA ® bioreactor was 5 and 15 min for every 4 h. The results showed that 15 min immersion for every 4 h increased the number of A. malaccensis shoot regeneration. Nonetheless, no significance difference was observed on biomass acquisition in both bubble column bioreactor and TIS-RITA ® bioreactor. Therefore, our findings indicate that immersion period was more critical than aeration rate for A. malaccensis shoot cultivation.