This study investigated the effects of microclimate conditions on the activity ofTetragonula laeviceps,Tetragonula biroi, andTetragonula dreschericultivated in ModularTetragonulaHives for producing crude propolis. The hives were equipped with sensors that recorded microclimate data within the hive as well as the total activity of bees entering and leaving the hives. This study also investigated the effects of cultivatingT. laeviceps,T. drescheri, andT. biroiwithP. merkusiiresin towards the productivity of crude propolis and the effects of different extraction methods on the yield, total phenolic content, total flavonoid content, and antibacterial activity of propolis extract produced by theTetragonulaspp. Based on the statistical analysis, there is a significant positive correlation between temperature and light intensity towards the activityTetragonulaspp. entering and leaving the beehives. The productivity of crude propolis lies in the range of 1.22–5.88 g/colony/week whereas the yield of propolis extract varies from 15.12 to 24.17%. The total phenolic and flavonoid content of the propolis extract lies in the range of 123.81–343.93 mg GAE/g and 5.48–35.77 mg QE/g, respectively. The highest propolis yield (32.45 ± 0.90%) was obtained from the crude propolis produced byT. drescherifollowed by Soxhlet extraction method. Propolis extract with the highest phenolic content (343.93 ± 44.32 mg GAE/g) and flavonoid content (35.77 ± 9.94 mg QE/g) was obtained from the propolis produced byT. laevicepsfollowed by maceration method. All the propolis extracts inhibited the growth ofStaphylococcus aureuswith the inhibition diameter varies from 6.58 ± 0.04 mm to 9.70 ± 0.7 mm which be considered as moderate antimicrobial activity.