Polylactic acid (PLA) and hydroxyapatite (HA) composite scaffolds have been widely studied for applications in bone tissue engineering (BTE) due to their bioactive and biocompatible properties. However, there is a need for more knowledge about the influence of size and crystallinity of HA nanoparticles (nHA) on the properties of PLA/nHA nanocomposite scaffolds produced by 3D printing. In this study, 3D printing was used to produce PLA nanocomposite scaffolds incorporated with nHA filler with different particle sizes and crystallinities. Initially, the nanocomposites were prepared by casting for 3D printing of scaffolds, which were characterized by analysis of thermal, morphological, physical-chemical, mechanical, and biological properties in vitro. The results showed that the size and crystallinity of nHA particles mainly influenced the scaffolds' mechanical properties, degradation rate, and bioactivity. Incorporating nHA provided a gain in compressive strength compared to pure PLA, superior to natural cancellous bone, which varies between 2 and 12 MPa. The lower crystallinity, 39.46 %, promoted a higher rate of degradation and bioactivity in vitro due to its solubility in the simulated fluid. All nanocomposite scaffolds showed cell viability above 90 %. The scaffolds showed suitable properties for BTE applications.