We present a semi-analytical model of dark matter subhalos that consistently incorporates (i) the properties of dark matter particles (e.g. kinetic decoupling), (ii) the properties of the primordial power spectrum of density fluctuations, and (iii) mass loss and potential disruption due to tidal stripping in galaxies (for which the detailed content and distributions of baryonic components strongly matter). This model allows to account for changes in the dark matter candidate properties as well as in the cosmological setup. We show applications to indirect dark matter searches for WIMP dark matter, though it could be applied to other observables related to gravitational effects (lensing, kinematics or dynamics) for other dark matter candidates.