We present a coarse-graining (or model order reduction) procedure for stochastic matrices by clustering. The method is consistent with the natural structure of Markov theory, preserving positivity and mass, and does not rely on any tools from Hilbert space theory. The reconstruction is provided by a generalized Penrose-Moore inverse of the coarse-graining operator incorporating the inhomogeneous invariant measure of the Markov matrix. As we show, the method provides coarse-graining and reconstruction also on the level of tensor spaces, which is consistent with the notion of an incidence matrix and quotient graphs, and, moreover, allows to coarse-grain and reconstruct fluxes. Furthermore, we investigate the connection with functional inequalities and Poincaré-type constants.