Frustrated bilayer quantum magnets have attracted attention as flat-band spin systems with unconventional thermodynamic properties. We study the low-temperature properties of a frustrated honeycomb-lattice bilayer spin-$frac{1}{2}$ isotropic ($XXX$) Heisenberg antiferromagnet in a magnetic field by means of an effective low-energy theory using exact diagonalizations and quantum Monte Carlo simulations. Our main focus is on the magnetization curve and the temperature dependence of the specific heat indicating a finite-temperature phase transition in high magnetic fields.