Homogenous dispersion of nanoparticles in polymer matrices is a technical challenge that if overcome can lead to improved mechanical properties of the resulting nanocomposites. In this work, we successfully refined commercially-available nanoscale, calcium deficient, and poorly crystalline hydroxyapatite (nHA) particles and composited them with acrylate and methacrylate functionalized soybean oil (mAESO) and triethylene glycol dimethacrylate (TEGDMA) producing inks for masked stereolithography (mSLA) -based 3D printing. First, we used shear mixing and ultrasonication on nHA/ethanol mixtures to break down agglomerates and then separated the finest nanoparticles from the remaining agglomerates using centrifugation. The refined nanoparticles (termed fine) were then mixed with the resins and UV-initiator to produce inks for 3D printing. Similarly, we prepared one ink using as-purchased nHA particles (termed raw) and another ink using leftover agglomerates after refinement (termed coarse). We compared the rheological properties of the nHA-resin inks. We used mSLA to fabricate nanocomposite specimens and tested them using flexural, and Mode-I fracture toughness testing following ASTM standards. The dispersion of nanoparticles in the polymer matrix was studied by analyzing backscattered mode scanning electron microscopy images. The nHA particle refinement improved the nanoparticle dispersion in the resin matrix while also increasing the viscosity and shear yield strength of the nanocomposite ink. The flexural fracture strength, flexural modulus, and Mode-I fracture toughness of refined nHA-based nanocomposites were increased by 11 %, 71 %, and 12 %, respectively compared to the raw nHA-based nanocomposites. However, the flexural fracture strain of refined nHA-based nanocomposites was lower by 40 % compared to the raw nHA-based nanocomposites. The nanocomposites became stiffer with the incorporation of refined nanoscale nHA. The separation of nanoscale nHA particles, excellent dispersion of these nanoparticles in polymer matrix, and improved flexural strength and modulus opens a new avenue towards the 3D printing of high-performance nHA-based nanocomposites.