The present work provides insight into the effect of connectivity within isomeric 1,2-bis(2-pyridylethynyl)benzene (bpb) palladium complexes on their electron transmission properties within gold|single-molecule|gold junctions. The ligands 2,2′-((4,5-bis(hexyloxy)-1,2-phenylene)bis(ethyne-2,1-diyl))bis(4-(methylthio)pyridine) (Lm) and 6,6′-((4,5-bis(hexyloxy)-1,2-phenylene)bis(ethyne-2,1-diyl))bis(3-(methylthio)pyridine) (Lp) were synthesized and coordinated with PdCl2 to give the trans-Pd(Lm or p)Cl2 complexes. X-ray photoelectron spectroscopy (XPS) measurements shed light on the contacting modes of the molecules in the junctions. A combination of scanning tunneling microscopy–break junction (STM–BJ) measurements and density functional theory (DFT) calculations demonstrate that the typical lower conductance of meta- compared with para-connected isomers in a molecular junction was suppressed upon metal coordination. Simultaneously there was a modest increase in both conductance and Seebeck coefficient due to the contraction of the HOMO–LUMO gap upon metal coordination. It is shown that the low Seebeck coefficient is primarily a consequence of how the resonances shift relative to the Fermi energy.