The human angiotensin-converting enzyme 2 (hACE2) serves as the primary receptor for SARS-CoV-2 entry via its interaction with the viral spike (S) protein. While certain ACE2 alleles are associated with enhanced binding affinity to the spike receptor-binding domain (RBD), the broader impact of ACE2 polymorphisms on infection susceptibility remains unclear. Building on previous findings that residues G496 and F497 in the spike protein and D355 and Y41 in ACE2 are critical for RBD–ACE2 binding, we employed computational saturation mutagenesis to systematically evaluate the effects of all possible ACE2 missense mutations on spike stability and binding. Our computational screening of ACE2 polymorphisms identified mutations at glycine residues (G268, G399, G405, G486, and G561) as having the most destabilizing effects on protein stability. We identified key residues that modulate binding affinity and pinpointed six ACE2 regions (residues 19–49, 65–102, 320–333, 348–359, 378–395, and 552–563) as candidate neutralizing peptides. Experimental assays confirmed that several of these peptides bind the spike protein and inhibit SARS-CoV-2 infection in ACE2-expressing cells. Comparative structural analysis between Wuhan and Omicron S1–ACE2 complexes revealed conserved binding patterns, indicating that these peptides may retain inhibitory potential across SARS-CoV-2 variants. These findings underscore the importance of considering host genetic diversity in understanding SARS-CoV-2 susceptibility and highlight the potential for designing ACE2-derived neutralizing peptides to block viral entry.