Many theories of dark matter beyond the Weakly Interacting Massive Particles (WIMP) paradigm feature an enhanced matter power spectrum on sub-parsec scales, leading to the formation of dense dark matter minihaloes. While these minihaloes are currently weakly constrained, future local observations, through a variety of techniques, may strongly constrain such substructures. The survival probability of those dense minihaloes in the Milky Way environment is crucial for interpreting local observations. In this work, we investigate two disruption effects: stellar disruption and (smooth) tidal disruption. These two mechanisms are studied using semi-analytic models and idealized N-body simulations. For stellar disruption, we perform a series of N-body simulations of isolated minihalo-star encounters to test and calibrate analytic models of stellar encounters, and apply the model to the realistic Milky Way disk environment. For tidal disruption, we also perform N-body simulations to confirm the effectiveness of the analytic treatment. Finally, we propose a framework to combine the stellar and tidal disruption of minihaloes with an orbit model, using it to make predictions for the overall survival probability of minihaloes in the Milky Way. We find the survival fraction for dense dark matter minihaloes, e.g. for axion miniclusters and minihaloes from Early Matter Domination, is ∼ 70%, with the relatively low-mass, compact population surviving. The survival fraction is insensitive to the detailed model parameters. We discuss various implications for their mass functions and future detection prospects.