The scope of this work was to create, with melt mixing compounding process, novel nanocomposite filaments with enhanced properties that industry can benefit from, using commer-cially available materials, to enhance the performance of three-dimensional (3D) printed structures fabricated via fused filament fabrication (FFF) process. Silicon Dioxide (SiO₂) nanoparticles (NPs) were selected as fillers for a polylactic acid (PLA) thermoplastic matrix at various weight % (wt.%) concentrations, namely, 0.5, 1.0, 2.0 and 4.0 wt.%. Tensile, flexural and impact test specimens were 3D printed and tested according to international standards and their Vickers microhardness was also examined. It was proven that SiO₂ filler enhanced the overall strength at concentrations up to 1 wt.%, compared to pure PLA. Atomic force microscopy (AFM) was employed to investigate the produced nanocomposite extruded filaments roughness. Raman spectroscopy was performed for the 3D printed nanocomposites to verify the polymer nanocomposite structure, while thermogravimetric analysis (TGA) revealed the 3D printed samples’ thermal stability. Scanning electron microscopy (SEM) was carried out for the interlayer fusion and fractography morphological characterization of the specimens. Finally, the antibacterial properties of the produced nanocomposites were investigated with a screening process, to evaluate their performance against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus).