The human immunodeficiency virus (HIV) affects millions of people worldwide who rely on antiretroviral therapy to prevent the acquired immunodeficiency syndrome and halt further HIV transmission. HIV integrase (IN), one of the three retroviral enzymes, catalyzes the covalent insertion of a DNA copy of the HIV genome into host cell chromatin, an essential step in the viral replication cycle. Integration enables expression of a new generation of viral RNA genomes and subgenomic RNAs encoding viral proteins, and establishes the potential for latency, a major barrier to cure. Despite being considered initially to be “undruggable”, IN has been successfully targeted with small-molecule therapeutics, two classes of which are studied here. The strand transfer inhibitors (STIs), which block an essential step in IN catalysis, are FDA-approved and in widespread clinical use. Clinical resistance to STIs has been documented, motivating the design of new generations of STIs with high genetic barriers to resistance and novel approaches to targeting IN. The allosteric inhibitors of integrase (ALLINIs) bind to a site distinct from STIs and do not directly block catalysis, instead act by aberrantly polymerizing IN, disrupting virion maturation. The binding interface of ALLINIs and a structural explanation of their mechanism of action was recently reported by our group. Accurate structural and biochemical data are essential for ongoing drug development and efforts to understand mechanisms of resistance. Here, we report structural and biochemical advances that further our understanding of antiretrovirals targeting HIV IN. We have improved the resolution of structural models of IN·ALLINI polymers, extended these data to multiple members of this class of compounds, and revealed mechanisms of resistance. We have identified a promising clinical opportunity combining ALLINIs and STIs that exploits the hypersensitivity of STI-resistant IN to ALLINI inhibition. Through the creation of an improved in vitro model, we report structural and biochemical data that most closely recapitulates the form of IN found in vivo. Finally, we report progress toward structural and functional characterization of the catalytically active complex of IN and viral DNA, the intasome. Together, this body of work advances our understanding of a key step in the pathogenesis of HIV and provides a foundation for improvements to therapeutics.