Tunneling spectroscopy was used to characterize a series of junctions with para-substituted (SH, F, Cl, Br, and I) benzoic acid monolayers positioned between aluminum/aluminum oxide surfaces and Pb electrodes. The tunneling conductance spectra revealed several effects that can be attributed to the size and reactivity of the para-substituent. First, as the size of the halogen substituent increased from fluoro to iodo, the extent of Pb penetration through the monolayer to the substrate was diminished. The extent of penetration was observed as a shift in the conductance minimum toward higher bias voltage. In the case of the 4-fluoro substituent, there was significant penetration of Pb to the bottom interface, and the conductance minimum was observed near 140 mV. In the case of the 4-iodo substituent, there was minimal Pb penetration, and the conductance minimum was ∼20 mV. Second, when the para-substituent was a thiol group, the deposition of lead results in Pb−S bond formation, which was confirmed by the absence of the S−H stretching mode in inelastic tunneling spectroscopy. The effect of Pb−S bond formation was to inhibit Pb penetration and invert the barrier height, which resulted in a shift in the minimum conductance to a negative bias. These results highlight the importance of tunneling spectroscopy to better understand contacting details at the metal−molecule interface.