We propose an efficient numerical method to compute configuration averages of observables in disordered open quantum systems whose dynamics can be unraveled via stochastic trajectories. We prove that the optimal sampling of trajectories and disorder configurations is simply achieved by considering one random disorder configuration for each individual trajectory. As a first application, we exploit the present method to the study the role of disorder on the physics of the driven-dissipative Bose-Hubbard model in two different regimes: (i) for strong interactions, we explore the dissipative physics of fermionized bosons in disordered one-dimensional chains; (ii) for weak interactions, we investigate the role of on-site inhomogeneities on a first-order dissipative phase transition in a two-dimensional square lattice.
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