A local multi-energy system (LMES) is a decentralized energy system producing energy under multiple forms to satisfy the energy demand of a set of buildings located in its neighborhood. We study the problem of optimally designing an LMES over a multi-phase horizon. This problem is formulated as a large-size mixed-integer linear program with a block-decomposable structure involving mixed-integer sub-problems. We propose a new way to adapt a recently published framework for generalized Benders decomposition to our problem. This is done by exploiting the fact that the constraint matrix appearing in front of the first-stage variables in the coupling constraints is non-negative. The obtained generalized Benders decomposition algorithm relies on the use of a new type of non-convex Benders cuts involving indicator functions. We first prove that, under the assumption that all first-stage decision variables are integer and bounded, the finite and optimal convergence of our algorithm is guaranteed in theory. We then investigate how to obtain a good numerical performance in practice. Finally, we report the results of a computational study carried out on a real-life case study. These results show that the proposed algorithm clearly outperforms both a mathematical programming solver directly solving the problem as a whole and a state-of-the art hierarchical decomposition algorithm.