Bone tissue engineering has emerged as a promising strategy for the treatment of osseous fractures, defects, and ultimately diseases caused by, for example, bone tumor resection, accident trauma, and congenital malformation. Additive fabrication of stem cell-seeded, osteoconductive porous scaffolds has been an effective method in clinical practice for the treatment of bone pathologies (such as osteoporosis, osteoarthritis, and rheumatic diseases). Porosity is known to be one of the main morphological characteristics of bone tissues, which affects the functional performance of an implanted bone scaffold. Hence, in situ detection and quantification of scaffold porosity implemented to ensure functional integrity prior to implantation/surgery is an unavoidable need. The objective of this research work is to introduce a robust, image-based method for identification and subsequently characterization of the surface porosity and dimensional accuracy of additively manufactured bone tissue scaffolds, with a focus on pneumatic micro-extrusion (PME) process. It was observed that the presented method would be capable of detecting complex individual pores based on a micrograph. Using the proposed method, not only were scaffold pores detected, but also scaffold porosity was characterized on the basis of various defined quality metrics/traits (such as the relative standard deviation of distance to the nearest pore). The proposed method was validated by contrasting its performance in “surface pore detection” against that of a standard method, tested on a complex benchmark in four different simulated lighting environments. Besides, the performance of the method in terms of “pore filling” was compared to that of a standard method, tested on a real PME-fabricated bone scaffold. It was observed that the proposed method had a better performance in pore filling, detection, and consolidation. Overall, the outcomes of this work pave the way for high-resolution fabrication of patient-specific, structurally complex, and porous bone scaffolds with easily validatable, functional, and medical properties for the treatment of bone pathologies.