Polymer–filler interactions play a major role in determining the antibacterial activity of organoclay in nanocomposites. The objective of the current study was to determine the effect of polymer type on the antibacterial properties of an organically modified clay – cloisite 10A (C10A) – using poly-ε-caprolactone (PCL) and poly-L-lactic acid (PLA) polymeric systems. Nanocomposite characterization using atomic force microscopy (AFM) showed an increase in roughness upon addition of the clay mineral, and X-ray diffraction (XRD) showed intercalation of the selected polymers into the interlayer spaces of the clay. Transmission electron microscopy (TEM) analysis supported the XRD findings. C10A in PCL thin films enhanced the bactericidal activity against Staphylococcus aureus when compared to the C10A in PLA. The observed change could be the result of pronounced levels of interaction between the filler and polymer matrix in the C10A-PLA nanocomposite when compared to C10A-PCL. The higher interaction levels could hinder the diffusion of bactericidal agents from the nanocomposite membranes. The present study provided insight into the nature of interaction between nanocomposite components and its impact on bioactivity, which can have applications in terms of generating engineered antibacterial materials.