Polyether-ether-ketone (PEEK) biomaterial has been increasingly employed for orthopedic, trauma, spinal, and dental implants due to its biocompatibility and in vivo stability. However, a lack of bioactivity and binding ability to natural bone tissue has significantly limited PEEK for many challenging dental implant applications. In this work, nanocomposites based on PEEK reinforced with bioactive silicate-based bioceramics (forsterite or bioglass) as nanofillers were prepared using high energy ball milling followed by melt blending and compression molding. The influence of nanofillers type and content (10, 20 and 30 wt.%) on the crystalline structure, morphology, surface roughness, hydrophilicity, microhardness, elastic compression modulus, and flexural strength of the nanocomposites was investigated. The scanning electron microscopy images of the nanocomposites with low nanofillers content showed a homogenous surface with uniform dispersion within the PEEK matrix with no agglomerates. All nanocomposites showed an increased surface roughness compared to pristine PEEK. It was found that the incorporation of 20 wt.% forsterite was the most effective in the nanocomposite formulation compared with bioglass-based nanocomposites; it has significantly improved the elastic modulus, flexural strength, and microhardness. In vitro bioactivity evaluation, which used biomimetic simulated body fluid indicated the ability of PEEK nanocomposites loaded with forsterite or bioglass nanofillers to precipitate calcium and phosphate bone minerals on its surface. These nanocomposites are expected to be used in long-term load-bearing implant applications and could be recommended as a promising alternative to titanium and zirconia when used as a dental implant material.