We introduce an optimal transport topology on the space of probability measures over a fiber bundle, which penalizes the transport cost from one fiber to another. For simplicity, we illustrate our construction in the Euclidean case , where we penalize the quadratic cost in the second component. Optimal transport becomes then constrained to happen along fixed fibers. Despite the degeneracy of the infinitely-valued and discontinuous cost, we prove that the space of probability measures with fixed marginal in the second component becomes a Polish space under the fibered transport distance, which enjoys a weak Riemannian structure reminiscent of the one proposed by F. Otto for the classical quadratic Wasserstein space. Three fundamental issues are addressed: 1) We develop an abstract theory of gradient flows with respect to the new topology; 2) We show applications that identify a novel fibered gradient flow structure on a large class of evolution PDEs with heterogeneities; 3) We exploit our method to derive long-time behavior and global-in-time mean-field limits in a multidimensional Cucker-Smale-type alignment model with weakly singular coupling.