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Because electron transfer is often highly sensitive to bridge length and molecular conformation, changes in these can have a large impact on the conductance of single molecule electrical junctions. In this study, pH is used to control the conformation and effective bridge length of single molecule junctions containing the peptide sequence H(EL)5C (where H stands for histidine, E for glutamic acid, L for leucine, and C for cysteine). The ionizable glutamic acid residues in this peptide result in an oligo-peptide structure highly sensitive to pH. At low pH, the H(EL)5C bridge exists in its more compact α-helical state, while at high pH, deprotonation leads to electrostatic repulsion between the charged carboxylate groups of the glutamic acid residues, promoting more extended conformations. An scanning tunneling microscopy-based method is used to measure the single molecule conductance of Au|H(EL)5C|Au two-terminal junctions in buffered electrolyte solution at low pH (2) and higher pH (6.9). In its more compact α-helical state at low pH, a single molecule conductance of 1.7 nS has been recorded, with the conductance then dropping to below 0.10 nS when the pH is raised to 6.9. This large pH-controlled drop in conductance shows that oligo-peptides can provide particularly sensitive motifs for controlling long-range electron transfer.