Adeno-associated virus (AAV) is a widely used vehicle for gene delivery but a limitation to AAV gene therapy can be inefficient transgene expression from AAV vectors. One approach to improve AAV transduction has been to combine the vector with small molecule modulators that disrupt cellular pathways, which can also impact AAV integration. Recombinant AAV genomes primarily remain in episomes, but AAV integration events occur at a low frequency. These events can be genotoxic. Therefore, studies to investigate the impact of modulators on AAV transduction should be coupled with characterization of AAV integration. Here, we profile two small molecule drug classes. First, we evaluate the function of topoisomerase poisons, which are small molecules that stabilize topoisomerase complexes and DNA breaks. Second, we target SUMOylation. To date, small molecule inhibitors of SUMOylation have not been evaluated for AAV modulation, so we characterize the SUMOylation inhibitor drug TAK-981. We find that integration targeting was altered by topoisomerase poisons and favored near actively transcribed regions. Doxorubicin and etoposide, which specifically inhibit type II topoisomerases, are found to boost integration of AAV DNA. Using machine-learning inferences, we find that these integrations were found to be selectively favored near topoisomerase II binding sites. We also find that treatment with the SUMOylation inhibitor TAK-981 at delivery can increase AAV transgene expression in transformed human cells, in primary human cells, and in mice. In addition, TAK-981 can boost transgene expression when introduced at long times after initial AAV vector transduction regardless of whether mice had been treated previously. Collectively, our results demonstrate the variable effects of small molecule modulators. We discuss how these findings add to our current understanding of AAV vectors and ways by which drug co-delivery may benefit clinical outcomes of AAV gene therapy.