Molecular components with their inherent scalability are expected to be promising supplements for nanoscale electronic devices. Here we report on how to specifically tune the electronic structure of chemisorbed molecules and thus to gain control of molecular transport properties. The electronic structure of our prototype π-conjugated carboxylic acid anchored on the Cu(110) surface is modified systematically by inserting nitrogen atoms in a six-membered aromatic ring, a carboxylic functional group at the aromatic ring or both. Depending on the specific nature of the substituent, the relative position of the occupied or unoccupied electronic states with respect to the Fermi level can be specifically controlled and thus the transport properties of the studied molecular systems are modified intentionally, as proven by our scanning tunneling spectroscopy measurements. On the basis of the insight gained by our systematic experiment and first-principles calculations we are also able to predict the specific molecular character (σ or π) of the orbitals involved in the transport process of a carboxylate-Cu(110) system, depending on the functionalization pattern employed.