It is important to understand how the supramolecular structure of molecular junctions affects their performance. Such studies are challenging because it is difficult to separate electronic effects from supramolecular structural effects because both depend on each other. Here we show that by changing the connector group that connects the active component (a ferrocene unit) of a molecular diode to the backbone (an alkyl chain), both the electronic and supramolecular structures of the junctions are modified. The connector group determines the tilt angle of the Fc unit which in turn affects the packing structure of the molecular diodes. In this case, the supramolecular structure dominates over the electronic structure of the molecular diodes, and junctions with loosely packed SAMs result in poorly performing molecular diodes, while stiff, densely packed SAMs result in well-performing molecular diodes.