Globally, malaria in recent years has witnessed a decline in the number of cases and death, though the most recent world malaria report shows a slight decrease in the number of cases in 2018 compared to 2017 and, increase in 2017 compared to 2016. Africa remains the region with the greatest burden of the disease. Cameroon is among the countries with a very high burden of malaria, with the coastal and forest regions carrying the highest burden of the disease. Nkongho-mbeng is a typical rural setting in the equatorial rain forest region of Cameroon, with no existing knowledge of the epidemiology of malaria in this locality. This study aimed at determining the current status of malaria epidemiology in Nkongho-mbeng. A cross-sectional survey was conducted, during which blood samples were collected from 500 participants and examined by microscopy. Risk factors such as, age, sex, duration of stay in the locality, housing type, environmental sanitation and intervention strategies including use of, LLINs and drugs were investigated. Trends in malaria morbidity were also determined. Of the 500 samples studied, 60 were positive, giving an overall prevalence of 12.0% with the prevalence of asymptomatic infection (10.8%), more than quadruple the prevalence of symptomatic infections (1.2%) and, fever burden not due to malaria was 1.4%. The GMPD was 6,869.17 parasites/μL of blood (95% C.I: 4,977.26/μL– 9,480.19/μL). A LLINs coverage of 84.4% and 77.88% usage was observed. Unexpectedly, the prevalence of malaria was higher among those sleeping under LLINs (12.56%) than those not sleeping under LLINs (8.97%), though the difference was not significant (p = 0.371). Being a male (p = 0.044), being unemployed (p = 0.025) and, living in Mbetta (p = 0.013) or Lekwe (p = 0.022) and the presence bushes around homes (p = 0.002) were significant risk factors associated with malaria infection. Trends in proportion demonstrated that, the prevalence of malaria amongst patients receiving treatment in the health center from 2015 to 2019 decreased significantly (p < 0.001) and linearly from 9.74% to 3.08% respectively. Data generated from this study can be exploited for development of a more effective control measures to curb the spread of malaria within Nkongho-mbeng.