In the endoplasmic reticulum (ER) of human cells, ERO1␣ and protein-disulfide isomerase (PDI) constitute one of the major electron flow pathways that catalyze oxidative folding of secretory proteins. Specific and limited PDI oxidation by ERO1␣ is essential to avoid ER hyperoxidation. To investigate how ERO1␣ oxidizes PDI selectively among more than 20 ERresident PDI family member proteins, we performed docking simulations and systematic biochemical analyses. Our findings reveal that a protruding -hairpin of ERO1␣ specifically interacts with the hydrophobic pocket present in the redox-inactive PDI b-domain through the stacks between their aromatic residues, leading to preferred oxidation of the C-terminal PDI a-domain. ERO1␣ associated preferentially with reduced PDI, explaining the stepwise disulfide shuttle mechanism, first from ERO1␣ to PDI and then from oxidized PDI to an unfolded polypeptide bound to its hydrophobic pocket. The interaction of ERO1␣ with ERp44, another PDI family member protein, was also analyzed. Notably, ERO1␣-dependent PDI oxidation was inhibited by a hyperactive ERp44 mutant that lacks the C-terminal tail concealing the substrate-binding hydrophobic regions. The potential ability of ERp44 to inhibit ERO1␣ activity may suggest its physiological role in ER redox and protein homeostasis.