Antibiotic resistance in pathogenic bacteria is a major health challenge, as Infectious Diseases Society of America (IDSA) has recognized that the past simply drugs susceptible pathogens are now the most dangerous pathogens due to their nonstop growing resistance towards conventional antibiotics. Therefore, due to the emergence of multi-drug resistance, the bacterial infections have become a serious global problem. Acute infections feasibly develop into chronic infections because of many factors; one of them is the failure of effectiveness of antibiotics against superbugs. Modern research of two-dimensional nanoparticles and biopolymers are of great interest to attain the intricate bactericidal activity. In this study, we fabricated an antibacterial nanocomposite consisting of representative two-dimensional molybdenum disulfide (2D MoS2) nanoparticles. Polyhydroxyalkanoate (PHA) and chitosan (Ch) are used to encapsulate MoS2 nanoparticles into their matrix. This study reports the in vitro antibacterial activity and host cytotoxicity of novel PHA-Ch/MoS2 nanocomposites. PHA-Ch/MoS2 nanocomposites were subjected to time-dependent antibacterial assays at various doses to examine their antibacterial activity against multi-drug-resistant Escherichia coli K1 (Malaysian Type Culture Collection 710859) and methicillin-resistant Staphylococcus aureus (MRSA) (Malaysian Type Culture Collection 381123). Furthermore, the cytotoxicity of nanocomposites was examined against spontaneously immortalized human keratinocyte (HaCaT) cell lines. The results indicated significant antibacterial activity (p value < 0.05) against E. coli K1 and MRSA. In addition, PHA-Ch/MoS2 showed significant host cytocompatibility (p < 0.05) against HaCaT cells. The fabricated PHA-Ch/MoS2 nanocomposites have demonstrated effective antibacterial activity against both Gram-positive and -negative bacteria and exhibited better biocompatibility. Finally, PHA-Ch/MoS2 nanocomposites are shown to be suitable for antibacterial applications and also hold potential for further biomedical studies.