The incidence of osteochondral lesions, as well as osteoarthritis of the ankle joint following osteochondritis dissecans and trauma, has been reappraised in recent years. Consequently, an increasing number of surgical interventions using different cartilage repair techniques is performed in the ankle joint, which has resulted in a growing demand for repetitive and objective assessment of cartilage tissue and its repair. While morphological imaging does enable monitoring of macroscopic changes with increasing precision, it fails to provide information about the ultrastructural composition of cartilage. The significance of molecular changes in cartilage matrix composition, however, is increasingly recognized, as it is assumed that macroscopic cartilage degeneration is preceded by a loss in glycosaminoglycans and a disorganization of the collagen network. Recent advances in biochemical magnetic resonance imaging (MRI) have yielded sequences sensitive to these changes, thus providing invaluable insight into both early cartilage degeneration and maturation of repair tissue, on a molecular level. The aim of this review was to provide a comprehensive overview of these techniques, including water and collagen-sensitive T2/T2* mapping, as well as glycosaminoglycan-sensitive sequences such as delayed gadolinium-enhanced MRI of cartilage dGEMRIC, and sodium imaging, and describe their applications for the ankle joint.