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Baryons and cold dark matter (CDM) did not comove prior to recombination. This leads to differences in the local baryon and CDM densities, the so-called baryon-CDM isocurvature perturbations $δ_{bc}$. These perturbations are usually neglected in the analysis of Large-Scale Structure data but taking them into account might become important in the era of high precision cosmology. Using gravity-only 2-fluid simulations we assess the impact of such perturbations on the dark matter halos distribution. In particular, we focus on the baryon fraction in halos as a function of mass and large-scale $δ_{bc}$, which also allows us to study details of the nontrivial numerical setup required for such simulations. We further measure the cross-power spectrum between the halo field and $δ_{bc}$ over a wide range of mass. This cross-correlation is nonzero and negative which shows that halo formation is impacted by $δ_{bc}$. We measure the associated bias parameter $b_{δ_{bc}}$ and compare it to recent results, finding good agreement. Finally we quantify the impact of such perturbations on the halo-halo power spectrum and show that this effect can be degenerate with the one of massive neutrinos for surveys like DESI.