We characterize electron transport across Au–molecule–Au junctions of heterogeneous carboxyl and methyl sulfide terminated saturated and conjugated molecules. Low-bias conductance measurements are performed using the scanning tunneling microscopy based break-junction technique in the presence of solvents and at room temperature. For a series of alkanes with 1–4 carbon atoms in the hydrocarbon chain, our results show an exponential decrease in conductance with increasing molecule length characterized by a decay constant of 0.9 ± 0.1 per methylene group. Control measurements in pH 11 solutions and with COOMe terminations suggest that the carboxylic acid group binds through the formation of a COO⁻–Au bond. Simultaneous measurements of conductance and force across these junctions yield a rupture force of 0.6 ± 0.1 nN, comparable to that required to rupture a Au–SMe bond. By establishing reliable, in situ junction formation, these experiments provide a new approach to probe electronic properties of carboxyl groups at the single molecule level.