Bone regeneration using Bone Morphogenetic Proteins (BMPs) alongside various engineered scaffolds has attracted considerable attention over the years. The field has seen extensive research in preclinical animal models, leading to the approval of two products and guiding the quest for new materials. Natural and synthetic polymers, ceramics, and composites have been used to fabricate the necessary porous 3D scaffolds and delivery systems for BMPs. Interestingly, all reported applications in the literature are triumphant. Evaluation of the results is typically based on histologic assessment after appropriate staining and radiological modalities, providing morphological identification of the newly formed bone and describing cells and the organic compound. Remarkably, while these evaluation methods illustrate mineralization, they are not capable of identifying hydroxyapatite crystals, the mineral component of the bone, which are crucial for its mechanical properties, structure, integrity, and long-term stability of regenerated bone tissue. This review aims to focus on the different scaffolds used in bone tissue engineering applications and underline the pressing need for techniques that could recognize the presence of hydroxyapatite crystals as well as their characteristics in bone tissue engineering, which will provide a more complete and comprehensive assessment of the successful results.