This study assesses malaria prevention and treatment behaviour among people living with HIV/AIDS (PLWHA) in Owerri, South Eastern Nigeria. Although Nigeria bears one of the world's largest burdens of both malaria and HIV, there is almost no research studying how co-infected patients manage their care. We systematically sampled 398 PLWHA receiving care at Imo State Specialist Hospital and the Federal Medical Centre in Owerri to complete a structured, pre-tested questionnaire on malaria care-seeking behaviour. Descriptive statistics were reported and chi-square tests and multivariate logistic regressions were also used. The majority of HIV-infected patients (78.9%) reported having had an episode of suspected malaria quarterly or more often. There was a large variation in care-seeking patterns: on suspicion of malaria, 29.1% of participants engaged in self-medication; 39.2% went to drug shops, and only 22.6% visited HIV/AIDS care centres. Almost 40% waited more than 24 hours before initiating treatment. Most (60.3%), reported taking recommended artemisinin-based combination treatments (ACT) but a significant minority took only paracetamol (25.6%) or herbal remedies (3.5%). Most (80%) finished their chosen course of treatment; and completion of treatment was significantly associated with the frequency of suspected malaria occurrence (p = 0.03). Most (62.8%) did not take anti-malaria medication while taking antiretroviral treatment (ART) and almost all (87.6%) reported taking an ACT regimen that could potentially interact with Nigeria's first-line ART regimen. Our findings suggest the need to pay more attention to malaria prevention and control as a crucial element in HIV/AIDS management in this part of Nigeria and other areas where malaria and HIV/AIDS are co-endemic. Also, more research on ART-ACT interactions, better outreach to community-level drug shops and other private sector stakeholders, and clearer guidelines for clinicians and patients on preventing and managing co-infection may be needed. This will require improved collaboration between programmes for both diseases.