Background In Australia, the preventative use of antiretroviral drugs [pre-exposure prophylaxis (PrEP) and treatment as prevention] is being embraced to protect individuals at high risk of HIV and reduce onward transmission. Methods: The adaptation of a behavioural surveillance system, the Gay Community Periodic Surveys, was reviewed to monitor the uptake and effect of new prevention strategies in Australia’s primary HIV-affected population (gay and bisexual men, GBM). The national trends in key indicators during 2000–15 were reviewed and a new measure to take account of antiretroviral-based prevention was developed. Results: Between 2000 and 2015, there were significant increases (P < 0.001) in annual HIV testing (56.1–64.8%), condomless sex with casual partners (26.8—38.8%) and the proportion of HIV-positive men on HIV treatment (72.5–88.4%) and with an undetectable viral load (73.7–94.7%). The proportion of casual partners who were HIV negative, not on PrEP and who engaged in receptive condomless sex also increased between 2000 and 2015 from 12.8 to 19.3%. Two scenarios anticipating the effect of PrEP highlighted the need to target GBM who engage in receptive condomless sex while also sustaining condom use at a population level. Conclusions: Behavioural surveillance can be successfully adapted to follow the effect of antiretroviral-based prevention. It is anticipated that HIV testing and HIV treatment will continue to increase among Australian GBM, but to prevent new infections, intervention in the growing proportion of GBM who have condomless sex with casual partners is needed. For PrEP to have its desired effect, condom use needs to be sustained.