Background: The global burden of sexually transmitted infections (STIs) poses a challenge in the context of HIV pre-exposure prophylaxis (PrEP) programmes. We aimed to explore factors associated with prevalent, incident, and recurrent STIs in men who have sex with men (MSM) and transgender women on PrEP in Brazil, Mexico, and Peru. Methods: ImPrEP was a prospective, single-arm, open-label, multicentre study that enrolled MSM and transgender women in the context of the public health systems of Brazil (14 sites), Mexico (four sites), and Peru (ten sites) between February, 2018, and June, 2021. Eligibility criteria followed regional PrEP guidelines at the study start, including participants aged 18 years and older, not living with HIV, and reporting at least one of the following in the previous 6 months: condomless anal sex (CAS), anal sex with partner(s) living with HIV, any bacterial STI, or transactional sex. Eligible participants were screened and enrolled on the same day to receive daily oral PrEP (tenofovir disoproxil fumarate 300 mg and emtricitabine 200 mg). We assessed three outcomes: prevalent bacterial STIs, incident bacterial STIs, and recurrent bacterial STIs. Testing occurred at baseline and quarterly for syphilis, anorectal chlamydia, and anorectal gonorrhoea. Behavioural data were collected at baseline and quarterly. The study was registered with the Brazilian Registry of Clinical Trials, U1111-1217-6021. Findings: Among all 9509 participants included in the ImPrEP study (3928 [41·3%] in Brazil, 3288 [34·6%] in Mexico, and 2293 [24·1%] in Peru), 8525 (89·7%) had available STI results at baseline and were included in the prevalent STI analysis, and 7558 (79·5%) had available STI results during follow-up and were included in the incident and recurrent STI analyses. 2184 (25·6%) of 8525 participants had any bacterial STI at baseline. STI incidence during follow-up was 31·7 cases per 100 person-years (95% CI 30·7-32·7), with the highest rate for anorectal chlamydia (11·6 cases per 100 person-years, 95% CI 11·0-12·2), followed by syphilis (10·5 cases per 100 person-years, 9·9-11·1) and anorectal gonorrhoea (9·7 cases per 100 person-years, 9·2-10·3). Although only 2391 (31·6%) of 7558 participants had at least one STI during follow-up, 915 (12·1%) participants had recurrent diagnoses, representing 2328 (61·2%) of 3804 incident STI diagnoses. Characteristics associated with prevalent, incident, and recurrent STIs included younger age, multiple sex partners, receptive CAS, substance use, and previous STI diagnoses at baseline (incident or recurrent only). Interpretation: Our findings underscore the nuanced dynamics of STI transmission among MSM and transgender women across Latin America, highlighting an urgent need for tailored interventions to mitigate STI burden effectively, especially among the most susceptible individuals.