Polyetheretherketone (PEEK) is a high-performance polymer; however, it is bioinert. Hence, in this study, we created a novel bioactive ceramic known as amorphous magnesium phosphate nanoparticles and incorporated it into PEEK using ball milling. We analyzed the influence of milling parameters, such as speed, duration, and the ball-to-powder ratio (BPR), on the extent of AMP mixing in PEEK. Our results indicate that 300 rpm and 2h were optimum to homogenously disperse AMP in PEEK. Interestingly, we noticed a decrease in the crystallinity of the unfilled PEEK and an increase in the crystallinity of the PEEK-AMP composite post-milling. Finally, a lower BPR such as 2:1 was apt for dispersing the AMP particles in PEEK. Overall, our study provides a comprehensive analysis of the influence of milling parameters on the mixing of the novel AMP in PEEK and determines an optimized set of milling parameters for developing bioactive PEEK-AMP composites.