Bone defects are common and, in many cases, challenging to treat. Tissue engineering is an interdisciplinary approach with promising potential for treating bone defects. Within tissue engineering, three-dimensional (3D) printing strategies have emerged as potent tools for scaffold fabrication. However, reproducibility and quality control are critical aspects limiting the translation of 3D printed scaffolds to clinical use, which remain to be addressed. To elucidate the factors that yield to the generation of defects in bioprinting and to achieve reproducible biomaterial printing, the objective of this article is to frame a systematic approach for optimizing and validating 3D printing of poly(caprolactone) (PCL)-hydroxyapatite (HAp) composite scaffolds. We delineate the effect of PCL-to-HAp ratio, print velocity, print temperature, and extrusion pressure on the architectural and mechanical properties of the 3D printed scaffold. Furthermore, we present an in situ image-based monitoring approach to quantify key quality-related aspects of constructs, such as the ability to deposit material consistently and print elementary shapes with fewer flaws. Our results show that small defects generated during the printing process have a significant role in lowering the mechanical properties of 3D printed polymeric scaffolds. In addition, the in vitro osteoinductivity of the fabricated scaffolds is demonstrated.