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Abstract We present cosmological dark matter (DM)–only zoom-in simulations of a Milky Way analog originating from enhanced linear matter power spectraP(k) relative to the standard cold, collisionless DM (CDM) cosmology. We consider a Gaussian power excess inP(k) followed by a cutoff in select cases; this behavior could arise from early-Universe physics that alters the primordial matter power spectrum or DM physics in the radiation-dominated epoch. We find that enhanced initial conditions (ICs) lead to qualitative differences in substructure relative to CDM. In particular, the subhalo mass function (SHMF) resulting from ICs with both an enhancement and a cutoff is amplified at high masses and suppressed at low masses, indicating that DM substructure is sensitive to features inP(k). Critically, the amplitude and shape of the SHMF enhancement depend on the wavenumber of theP(k) excess and the presence or absence of a cutoff on smaller scales. These alterations to the SHMF are mainly imprinted at infall rather than during tidal evolution. Additionally, subhalos are found systematically closer to the host center, and their concentrations are increased in scenarios withP(k) enhancement. Our work thus reveals effects that must be captured to enableP(k) reconstruction using DM substructure.