In-medium properties of the low-lying baryons are studied in the quark-meson coupling (QMC) model, focusing on the $Sigma_b$ and $Xi_b$ baryons. It is predicted that the Lorentz-scalar effective mass of $Sigma_b$ becomes smaller than that of $Xi_b$ at moderate nuclear matter density, and as the density increases, namely, $m^*_{Sigma_b} < m^*_{Xi_b}$, although in vacuum $m_{Sigma_b} > m_{Xi_b}$. We also study the effects of the repulsive Lorentz-vector potentials on the excitation energies of these bottom baryons.