This study focuses on the modification of halloysite nanotubes (diameter 30–70 nm and length 1–3 µ) using concentrated sulphuric acid to create modified HNTs (mHNTs) and investigates their impact on the properties of PEEK material. Co-rotating twin screw extrusion is employed to incorporate various loadings of mHNTs into the PEEK matrix. The experimental results demonstrate a significant increase in hardness, impact strength, elongation at break, tensile and flexural strengths, and tensile modulus with increasing mHNT concentration. The mHNTs function as bridging tools and reinforcing agents within the polar-nonpolar hybrid system, facilitating compatibility between the blend partners. The composites exhibit improved dynamic thermal and mechanical properties compared to the pure PEEK. The composite materials are further characterized using techniques such as TGA, FESEM, DSC, DMA and FTIR. The enhanced effects observed in the developed composites are attributed to improved interfacial adhesion and favorable interactions between the PEEK matrix and the mHNTs.