Maize flour is the staple food in many African countries, which is often contaminated with mycotoxin-producing fungi. In this study, fungal contamination and the concentrations of fumonisins B1 and B2 in different types of maize flour in Malawi were examined, and the risk of mycotoxicosis, including endemic cancer, development was assessed. Data on the maize flour consumption of 187 Malawians were collected using a self-generated questionnaire. Fifty-nine samples of four differently processed types of flour from home-grown maize were collected and screened for mycotoxins using high-performance liquid chromatography–mass spectrometry (HPLC-MS). Fumonisin B1 and B2 concentrations in maize flour and daily individual intakes were quantified by combined accelerated solvent extraction, solid phase extraction, and HPLC-MS detection. The fumonisin concentrations ranged from 0.00 to 10,306.65 μg/kg maize, with a median concentration of 230.20 μg/kg (interquartile range (IQR), 592.77), and differed significantly among the four flour types. The median daily intake of fumonisins B1 and B2 per kilogram body weight was 3.01 μg (IQR, 6.47) and was significantly greater for deya flour (8.17 μg (IQR, 12.84)) than for mgaiwa flour (3.73 μg (IQR, 6.23); p = 0.046), gramil flour (1.08 μg (IQR, 2.39); p = 0.030), and white flour (1.18 μg (IQR, 2.78); p = 0.002). This intake exceeded the legitimate upper limit in 75% of individuals, by about nine times on average. The reduction of fumonisin intake is crucial to lower the associated disease risk and burden and can be achieved by changing the kernel processing method, improving storage conditions, and introducing sorghum and millet as possible staple food alternatives in Malawi.