HIV-1 integrase (IN) is targeted by two classes of antivirals: integrase strand transfer inhibitors (INSTIs), which bind to the active site within the catalytic core domain (CCD), and allosteric integrase inhibitors (ALLINIs), which bind at the CCD dimer interface. ALLINIs were initially designed to disrupt interactions with the cellular cofactor LEDGF/p75, but it has become clear that ALLINIs primarily act by promoting formation of aberrant integrase polymers. The ALLINIs achieve this by stabilizing ectopic intermolecular interactions between the CCD dimer and the integrase carboxy-terminal domain (CTD), which disrupts viral maturation. Previously, we determined the structure of full-length HIV-1 IN bound to the ALLINI GSK1264 at 4.4 Å resolution, revealing its polymerization mechanism. More recently, we reported the X-ray crystal structure of a minimal ternary complex between CCD, CTD, and the ALLINI BI-224436 at a higher resolution. In this study, we improve the original 4.4 Å structure using this higher-resolution information and report two new structures of full-length HIV-1 IN harboring escape mutations in the CCD (Trp131Cys) or CTD (Asn222Lys) bound with the prototype ALLINI BI-D at 4.5 Å. These structures reveal perturbations to the tertiary organization associated with escape substitutions, which correlate with their reduced ability to form ectopic ALLINI-induced polymers in vitro. These findings suggest a general structural mechanism of ALLINI resistance and provide insights for the design of improved ALLINIs.