Since X-rays were discovered, in 1895, and since the first radiological image of a hand, bone tissue has been the subject of detailed medical imaging. However, advances in bone engineering, including the increased complexity of implant scaffolds, currently also underline the limits of X-ray imaging. Therefore, advanced follow-up imaging methods are pivotal to develop. The field of noninvasive, high-sensitivity, and high-resolution anatomical and functional imaging techniques (optical, ultrasound, positron emission tomography, single-photon emission computed tomography, magnetic resonance, etc.) offers a wide variety of tools that potentially could be considered as alternatives, or at least supportive, to the most commonly used X-ray computed tomography. Moreover, dedicated preclinical scanners have become available, with sensitivity and resolution even higher than clinical scanners, thus favoring a quick translation from preclinical to clinical applications. Furthermore, the armamentarium of bone-specific probes and contrast agents for each of this imaging modalities is constantly growing. This review focuses on such preclinical imaging tools, each with its respective strengths and weaknesses, used alone or in combination. Especially, multimodal imaging will dramatically contribute to improve the knowledge on bone healing regenerative processes.