Detrimental physical and mechanical properties are common problems for composites when their flame retardancy is improved through filler additions. An increased interest of the synergistic nanoparticle addition to improve the flame retardancy of natural fiber composites is the aim of this work. The paper investigates the synergistic effect of two different nanoparticles (halloysite nanotubes (HNTs) and montmorillonite (MMT) nanoclay) on the flame and mechanical properties in an intumescent ammonium polyphosphate (APP)-based polypropylene (PP)/kenaf composite system. First, the nature of nanoparticle dispersion in PP through Xray diffraction (XRD) and transmission electron microscopy (TEM) reveals that under twin screw compounding process, the partial exfoliation and intercalation have taken place within the nanocomposites. An increase in the decomposition temperature was observed under thermogravimetric analysis (TGA), with the presence of HNT. However, MMT tends to lower the maximum decomposition temperature under inert atmosphere. The flammability analysis in an intumescent flame retardant (IFR) system shows that the suitable amount of high aspect ratio nanoparticles with their exfoliation characteristics effectively helps to reduce the sustained combustion. Even though, improved stiffness properties can be observed with the presence of increased filler content, particle agglomeration tends to reduce the mechanical strengths of these composites due to low compatibilization and crack propagation.