Plasmon excitation in molecular tunnel junctions is interesting because the plasmonic properties of the device can be, in principle, controlled by varying the chemical structure of the molecules. The plasmon energy of the excited plasmons usually follows the quantum cutoff law, but frequently overbias plasmon energy has been observed, which can be explained by quantum shot noise, multielectron processes, or hot carrier models. So far, clear correlations between molecular structure and the plasmon energy have not been reported. Here, we introduce halogenated molecules (HS(CH 2 ) 12 X, with X = H, F, Cl, Br, or I) with polarizable terminal atoms as the tunnel barriers and demonstrate molecular control over both the excited plasmon intensity and energy for a given applied voltage. As the polarizability of the terminal atom increases, the tunnel barrier height decreases, resulting in an increase in the tunneling current and the plasmon intensity without changing the tunneling barrier width. We also show that the plasmon energy is controlled by the electrostatic potential drop at the molecule−electrode interface, which depends on the polarizability of the terminal atom and the metal electrode material (Ag, Au, or Pt). Our results give new insights in the relation between molecular structure, electronic structure of the molecular junction, and the plasmonic properties which are important for the development of molecular scale plasmonic-electronic devices.