Malaysia honey such as Tualang, Gelam and Acacia with broad nutraceutical and therapeutic effects and commonly used in the traditional treatment of human illness. However, proper antibacterial study of Malaysia honey against human pathogen still need to investigate to ensure their antibacterial properties. This study investigated the antimicrobial activity and antioxidant activity (AOA) of Malaysia honey against human pathogenic bacteria. The Tualang, Gelam and Acacia honey was encapsulated by using 5% maltodextrin powder through freeze-drying method, and the antimicrobial property of encapsulated honey were tested on the in vitro of S. aureus and E. coli was conducted using the broth test technique. The antibacterial activity results showed the higher value of encapsulated 2% Tualang honey with maltodextrin against S. aureus and E. coli were 4 mg/ml and 8 mg/ml respectively. Meanwhile, the AOA analysis show an encapsulated 2% Tualang honey have higher AOA, 4.3 mg/mL then Acacia honey (4.5 mg/mL) and Gelam honey (5.4 mg/mL). However, Tualang honey show a higher antibacterial activity of two type of bacteria, followed by Gelam honey and Acacia honey. The finding suggests that type of Malaysia honey has significant effect on their antibacterial property and antioxidant activity. Further research is needed to improve the encapsulation of active compound of honey by use different types of encapsulated shell material to enhance the antibacterial properties of Malaysia honey.