In this paper, we study the structure of the differential operator algebra \( \mathcal {D}(W) \) and its associated eigenvalue algebra \( \Lambda (W) \) for matrix-valued orthogonal polynomials. While \( \Lambda (W) \) is isomorphic to \( \mathcal {D}(W) \) , its simpler framework allows us to efficiently derive strong results about \( \mathcal {D}(W) \) and its center \( \mathcal {Z}(W) \) . We analyze the behavior of the center under Darboux transformations, establishing explicit relationships between the centers of Darboux-equivalent weights. These results are illustrated through the study of both reducible and irreducible matrix weights, including a detailed analysis of an irreducible Jacobi-type weight.