Systematic conductivity measurements in nanoscale junctions containing a self-assembled monolayer of conjugated molecules are reported. Different conductivity mechanisms are identified depending on the granularity of the metal used as a substrate for assembling the monolayer. Unexpectedly, the energy scale controlling the dominant conductance channels is quite low in comparison with the molecular level spacing. In single-grain junctions, the dominant conductance mechanism is hopping with an energy scale of the order of 10-100 meV determined by the nature of the metal contacts. In the case of multigrain junctions, additional tunnel conductance is observed with low-energy Coulomb-blockade features.