Additive manufacturing, particularly fused filament fabrication (FFF), enables the creation of polymer composites with precisely controlled mechanical properties. This control depends heavily on the mixing method during filament fabrication, which significantly impacts how reinforcing elements are distributed within the material. Despite its importance, a critical knowledge gap exists regarding how different mixing methods affect the mechanical properties of FFF-printed composites. This study evaluates three mixing methods—magnetic stirring (MS), wet speed mix (WSM), and dry speed mix (DSM) for polylactic acid-hydroxyapatite (PLA-HA) composites printed using the FFF method. The fabricated composites were assessed for mechanical properties using micro-indentation and isostatic compression tests, as well as topography and elemental composition via scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS), respectively. Micro-indentation revealed the highest elastic modulus, indentation hardness, and creep resistance for DSM samples. Isostatic compression tests also corroborated these findings, with DSM leading to higher modulus of elasticity, modulus of resilience, absorbed plastic energy, and achievable compressive stress. EDS analysis confirmed the presence of HA particles within the PLA matrix for all three sample types. Among these three widely used mixing procedures, the findings of this study suggest that the DSM mixing method holds promise for fabricating high-performance FFF-printed polymer composites. While this study is limited to PLA-HA composites, the approach may offer a pathway for exploring its application to other ceramic-reinforced polymer composites in future research.