We deal with isomorphic Banach-Stone type theorems for closed subspaces of vector-valued continuous functions. Let F = R or C. For i = 1, 2, let E i be a reflexive Banach space over F with a certain parameter λ(E i ) > 1, which in the real case coincides with the Schaffer constant of E i , let K i be a locally compact (Hausdorff) topological space and let H i be a closed subspace of C 0 (K i , E i ) such that each point of the Choquet boundary Ch H i K i of H i is a weak peak point. We show that if there exists an isomorphism T : H 1 → H 2 with T · T −1 < min{λ(E 1 ), λ(E 2 )}, then Ch H 1 K 1 is homeomorphic to Ch H 2 K 2 . Next we provide an analogous version of the weak vector-valued Banach-Stone theorem for subspaces, where the target spaces do not contain an isomorphic copy of c 0 .