Polyetheretherketone (PEEK) composites that incorporate hydroxyapatite (HA) and multiwalled carbon nanotubes (MWCNTs) exhibit significant potential for biomedical applications. Despite this, getting MWCNTs evenly distributed throughout the PEEK matrix remains challenging. This study investigates the effects of two ionic liquids (ILs) at varying quantities on the mechanical and biological characteristics of composites made of PEEK and MWCNTs. The concentrations of IL [EMIM]HSO4 (1-ethyl-3-methylimidazolium hydrogen sulfate) and IL [BMIM]Ac (1-methyl-3-butylimidazolium acetate) varied from 0.5 to 2 wt% to modify the MWCNTs. The modified MWCNTs were combined with PEEK and HA by melt-blending and thermal compression to create PEEK/MWCNTs/HA composite sheets. FESEM and optical micrographs showed ILs-modified MWCNTs dispersed homogeneously in PEEK. The composites of PEEK and MWCNTs that included 1 wt% [BMIM]Ac degraded at the maximum temperature (580.89°C) and provided the elastic modulus that was 35% greater than that of non-IL composites. The Alamar blue assay investigation confirmed that inclusion of HA to PEEK composites improved the cells viability (more than 80%). The results showed that ILs-based methods are environmentally friendly, and promising way to treat PEEK and HA for uniform MWCNTs dispersion, which could have future in biological applications.