For long time, osteoporosis (OP) was exclusively associated with an overall bone mass reduction, leading to lower bone strength and to a higher fracture risk. For this reason, the measurement of bone mineral density through dual X-ray absorptiometry was considered the gold standard method for its diagnosis. However, recent findings suggest that OP causes a more complex set of bone alterations, involving both its microstructure and composition. This review aims to provide an overview of the most evident osteoporosis-induced alterations of bone quality and a résumé of the most common imaging techniques used for their assessment, at both the clinical and the laboratory scale. A particular focus is dedicated to the micro-computed tomography (micro-CT) due to its superior image resolution, allowing the execution of more accurate morphometric analyses, better highlighting the architectural alterations of the osteoporotic bone. In addition, micro-CT has the potential to perform densitometric measurements and finite element method analyses at the microscale, representing potential tools for OP diagnosis and for fracture risk prediction. Unfortunately, technological improvements are still necessary to reduce the radiation dose and the scanning duration, parameters that currently limit the application of micro-CT in clinics for OP diagnosis, despite its revolutionary potential.