Misfolded or unassembled polypeptides in the endoplasmic reticulum (ER) are retro‐translocated into the cytosol and degraded by the ubiquitin–proteasome system. We reported previously that the SCF Fbs1,2 ubiquitin‐ligase complexes that contribute to ubiquitination of glycoproteins are involved in the ER‐associated degradation pathway. Here we investigated how the SCF Fbs1,2 complexes interact with unfolded glycoproteins. The SCF Fbs1 complex was associated with p97/VCP AAA ATPase and bound to integrin‐β1, one of the SCF Fbs1 substrates, in the cytosol in a manner dependent on p97 ATPase activity. Both Fbs1 and Fbs2 proteins interacted with denatured glycoproteins, which were modified with not only high‐mannose but also complex‐type oligosaccharides, more efficiently than native proteins. Given that Fbs proteins interact with innermost chitobiose in N ‐glycans, we propose that Fbs proteins distinguish native from unfolded glycoproteins by sensing the exposed chitobiose structure.