Bone defects are commonly caused by traumatic injuries and tumor removal and critically sized defects overwhelm the regenerative capacity of the native tissue. Reparative strategies such as auto, xeno, and allografts have proven to be insufficient to reconstruct and regenerate these defects. For the first time, we introduce the use of handheld melt spun three dimensional printers that can deposit materials directly within the defect site to properly fill the cavity and form free-standing scaffolds. Engineered composite filaments were generated from poly(caprolactone) (PCL) doped with zinc oxide nanoparticles and hydroxyapatite microparticles. The use of PCL-based materials allowed low-temperature printing to avoid overheating of the surrounding tissues. The in situ printed scaffolds showed moderate adhesion to wet bone tissue, which can prevent scaffold dislocation. The printed scaffolds showed to be osteoconductive and supported the osteodifferentiation of mesenchymal stem cells. Biocompatibility of the scaffolds upon in vivo printing subcutaneously in mice showed promising results. Statement of significance: • Bone defects are frequent and, in many cases, benefit from an immediate intervention. • A portable and handheld printer is introduced that allows the printing of hard polymeric materials directly into the defect site that allow reconstruction of the geometrical features of the defected tissue. • The ease-of-use of the investigated device was demonstrated both in vitro and in vivo. • The in situ printed scaffolds adhered to the tissue and supported the growth and differentiation of cultured stem cells. They also prevented bacterial growth without inducing excessive inflammation.