Additively manufactured implants, surgical guides, and medical devices that would have direct contact with the human body require predictable behaviour when stress is applied during their standard operation. Products built with Fused Filament Fabrication (FFF) possess orthotropic characteristics, thus, it is necessary to determine the properties that can be achieved in the XY- and Z-directions of printing. A concentration of 10 wt% of hydroxyapatite (HA) in polyetherketoneketone (PEKK) matrix was selected as the most promising biomaterial supporting cell attachment for medical applications and was characterized with an Ultimate Tensile Strength (UTS) of 78.3 MPa and 43.9 MPa in the XY- and Z-directions of 3D printing, respectively. The effect of the filler on the crystallization kinetics, which is a key parameter for the selection of semicrystalline materials suitable for 3D printing, was explained. This work clearly shows that only in situ crystallization provides the ability to build parts with a more thermodynamically stable primary form of crystallites.