Malaria remains a major health problem in Cameroon; It accounts for 38% of consultations, 24% of deaths and 36.8% of absenteeism in the country. The negative economic impact of malaria has encouraged a new control approach targeting companies. In this regard, a cross sectional study was conducted from February 2015 to June 2017 in 14 companies in the town of Douala. This study aimed at determining the prevalence, control practices of employees and identifying associated factors with malaria. A total of 2705 workers were interviewed and systematically screened for malaria using LED fluorescence microscopy (CyScope®). All positive cases were given a malaria treatment. The prevalence of malaria and asymptomatic malaria was 30.1% and 28.9% respectively; asymptomatic malaria accounted for 95.7% of all positive diagnostic test. Malaria infection was significantly higher in employees aged 36-60 years (30.5%) and having completed primary studies (36%). ITNs ownership and utilization were 86.36% and 77.23% respectively. The risk for malaria infection has significantly decreased with age and educational level while the employees' level of education and size of households were significantly associated with the regular utilization of ITNs. This is the first study assessing malaria prevalence and risk factors in workplace in Cameroon and using a novel diagnostic tool. This study outlines a high prevalence of malaria infection, especially asymptomatic carriage, high rates of ITNs ownership and utilization, as well as the influence of level of education, age and household size as associated factors. Active case detection of asymptomatic carriers through systematic screening of employees at workplace and their treatment is feasible with the Cyscope microscope and could be a good complement to ongoing control strategies.