Anaerobic digestion is a promising method to treat citrus waste. However, the presence of limonene in citrus waste inhibits anaerobic digestion process. Limonene is an antimicrobial compound and could inhibit methane forming bacteria that takes a longer time to recover than the injured acid forming bacteria. Hence, volatile fatty acids will be accumulated and methane production will be decreased. One way to solve this problem is by conducting anaerobic digestion process into two stages. The first step is aimed for hydrolysis, acidogenesis, and acetogenesis reactions and the second stage is aimed for methanogenesis reaction. The separation of the system would further allow each stage in their optimum conditions making the process more stable. In this research, anaerobic digestion was carried out in batch operations using 120 ml-glass bottle bioreactors in 2 stages. The first stage was performed in free-cells bioreactor, whereas the second stage was performed in both bioreactor of free cells and membrane bioreactor. In the first stage, the reactor was set into 'anaerobic' and 'semi-aerobic' conditions to examine the effect of oxygen on facultative anaerobic bacteria in acid production. In the second stage, the protection of membrane towards the cells against limonene was tested. For the first stage, the basal medium was prepared with 1.5 g VS of inoculum and 4.5 g VS of citrus waste. The digestion process was carried out at 55°C for four days. For the second stage, the membrane bioreactor was prepared with 3 g of cells that were encased and sealed in a 3×6 cm2polyvinylidene fluoride membrane. The medium contained 40 ml basal medium and 10 ml liquid from the first stage. The bioreactors were incubated at 55°C for 2 days under anaerobic condition. The results from the first stage showed that the maximum total sugar under 'anaerobic' and 'semi-aerobic' conditions was 294.3 g/l and 244.7 g/l, respectively. The corresponding values for total volatile fatty acids were 3.8 g/l and 2.9 g/l, respectively. Methane production of citrus waste taken from the first stage under 'anaerobic' condition in membrane and free-cells bioreactors was 11.2 Nml and 7.2 Nml, respectively. Whereas, methane production of citrus waste taken from the first stage under 'semi-aerobic' condition in membrane and free-cells bioreactors was 8.8 Nml and 5.7 Nml, respectively. It can be seen from the results of the first stage that volatile fatty acids from 'anaerobic' condition was higher than that of 'semi-aerobic' condition. The absence of oxygen provides the optimal condition for growth and metabolism of facultative and obligatorily anaerobic bacteria in the first stage. Furthermore, polyvinylidene fluoride membrane was able to protect the cells from antimicrobial compounds.