(1) Background: The autologous matrix-induced chondrogenesis (AMIC) is a bio-orthopedic treatment for articular cartilage damage. It combines microfracture surgery with the application of a collagen membrane. The aim of the present study was to report a medium-term follow-up of patients treated with AMIC for focal chondral lesions. (2) Methods: Fourty-eight patients treated surgically and 21 control participants were enrolled in the study. To evaluate the functional outcomes, the proprioceptive (postural stability, postural priority) and isokinetic (peak value of maximum knee extensor and flexor torque in relation to body mass and the total work) measurements were performed. To evaluate the clinical outcomes, the Lysholm score and the IKDC score were imposed. (3) Results: Compared to the preoperative values, there was significant improvement in the first 2 years after intervention in the functional as well as subjective outcome measures. (4) Conclusions: AMIC showed durable results in aligned knees.