Background/Objectives: Alkaptonuria (AKU) is a rare genetic disorder characterized by elevated levels of circulating homogentisic acid (HGA), which accumulates in connective tissues. The musculoskeletal system is particularly susceptible to HGA deposition, often resulting in severe ochronotic osteoarthropathy, especially in the hips, shoulders, knees, and spine. However, little is known about the effects of AKU on skeletal muscle tissue. The study aimed to evaluate changes in lower limb muscles associated with AKU. Methods: This case report describes the treatment of ochronotic osteoarthropathy in the knee of a 73-year-old male patient. Muscle properties were assessed using the MyotonPRO device. The rectus femoris, vastus medialis, and patellar tendon were examined both preoperatively and three months postoperatively. Results: Following total knee arthroplasty (TKA) of the right knee, the patient demonstrated significant improvement in functional outcomes. The MyotonPRO assessment revealed measurable differences in muscle properties between the operated and non-operated limbs. Postoperative measurements indicated improvements in muscle tone, elasticity, and viscoelastic parameters in the treated limb. Conclusions: This case report supports the effectiveness of TKA as a treatment for ochronotic osteoarthropathy. Furthermore, it is the first study to use the MyotonPRO to assess muscle and tendon properties in a patient with AKU. These findings highlight the need for further research into the muscular effects of this rare metabolic disorder.