Corneal collagen cross-linking is an established procedure for the treatment of certain eye diseases which is applied to enhance the mechanical stability of such biotissue without deteriorating its functionality. However, being transparent, the optical analysis of the outcome of such treatments is cumbersome and relies on relatively expensive experimental equipment. We aim to apply the Mueller matrix polarimetry for the detection of photo-induced collagen cross-linking in transparent biotissue after treatment with riboflavin and UV irradiation. A simple Mueller matrix polarimetry setup could provide a fast and non-invasive analysis of transparent media to sensitively detect small photo-induced cross-linking effects in biotissue. We demonstrated the current capabilities of the approach on non-planar porcine cornea samples ex vivo. We reported the distinction between untreated and riboflavin-treated samples. The differences observed were correlated with the variation of certain Mueller matrix elements and parameters derived from the decomposition. The measurement data show variation in the cross-linked and non-cross-linked samples, although the effect of the UV treatment on the riboflavin-treated samples was not at the same level of significance yet and needs further investigation. The Mueller matrix measurement represents a promising approach for the detection of the effects of corneal collagen cross-linking. Further studies with a larger sample number are required to validate this approach. In the future, this could enable the reliable and non-invasive detection of photo-induced effects in biotissue and open the possibility for in vivo application, e.g., in eye disease treatment or the detection of scar collagen development.