In the last few years, different tissue engineering strategies have been developed for the repair of osteochondral lesions. When the osteochondral scaffold is implanted on the femoral condyle, the meniscus might be affected by the implant and might undergo a progressive degeneration. The aim of our study is to analyze the morphological changes of the meniscus following an osteochondral lesion and the implant of a biphasic scaffold. A critical osteochondral defect was generated in the medial femoral condyle of mature sheep. Three defects were left untreated, the remaining lesions were divided into three groups and treated with a biphasic substituted formed by collagen type I and Wollastonite or Wollastonite/Hydroxyapatite. Animals were sacrificed after 6 months and menisci were isolated and analyzed by arthro-CT, macroscopic evaluation and histology. The results demonstrated that the osteochondral lesion negatively affects meniscus morphology and that the osteochondral substitute only partially mitigates the meniscus degeneration.