Introduction Malaria is a global health issue including in Indonesia. Currently, most of the cases was in the rural of eastern part of the country. However, malaria risk factors amongst rural adult were less documented. This study investigated malaria risk factors amongst rural adults in East Nusa Tenggara Province (ENTP). Methods A community based cross –sectional study was conducted to interview 1495 rural adults in ENTP. A multi-stage cluster random sampling technique was applied to collect data on malaria history, demographic, behavioural and environmental factors of malaria of participants. Logistic regression model was applied to decide significant factors associated with malaria. Results The prevalence of malaria was 13.4%. The prevalence of malaria was significantly higher for adults with low level of malaria knowledge (Adjusted odd ratio (AOR): 2.43, 95% confidence interval (CI): 1.38 — 4.27) compared to those with high malaria knowledge level, having moderate malaria knowledge level (AOR: 1.99, 95% CI: 1.11 — 3.57) compared to those high malaria knowledge level, having no education (AOR: 2.18, 95% CI: 1.37 — 3.45) compared to those junior high school or above education level, outdoor occupation (AOR: 1.81, 95% CI: 1.22 — 2.68) compared to indoor occupation, having family size > 4 (AOR 2.08, 95% CI: 1.52 —2.87) compared to those ≤ 4 Conclusion The study revealed the prevalence of malaria amongst rural adults in this province was high. The study highlights the power of malaria knowledge level on the prediction of malaria prevalence amongst rural adults. Health education intervention is critical for vulnerable groups to reduce malaria prevalence in the province.