In resource limited settings, malaria and undernutrition are major public health problems in pregnancy. Therefore, this study assessed the association between malaria infection and undernutrition among pregnant women in the Mount Cameroon area. This cross-sectional study enrolled 1,014 pregnant women consecutively over a year. A structured questionnaire was used to collect socio-demographic information and clinical data. Maternal nutrition was assessed using dietary diversity (DD). Peripheral blood samples collected were used for the diagnosis of malaria parasitaemia by microscopy whereas haemoglobin (Hb) levels were determined using an Hb meter. Logistic regression was used to determine factors associated with malaria and dietary diversity. The prevalence of malaria infection and undernutrition was 17.8% and 89.6% respectively. In addition, of those infected with malaria, geometric mean parasite density was 301/μL of blood (range: 40–9280) while mean DD score was 3.57±0.82 (range: 1–7). The odds of being infected with malaria parasitaemia was highest among women enrolled in the rainy season (OR = 1.58, P = 0.043), who were farmers (OR = 2.3, P = 0.030), had a household size of < 4 individuals (OR = 1.48, P = 0.026) and who were febrile (OR = 1.87, P < 0.001). Also, attending clinic visits in Mutengene Medical Centre (OR = 2.0, P = 0.012) or Buea Integrated Health Centre (OR = 2.9, P = < 0.001), being < 25 years (OR = 2.4, P = 0.002) and a farmer (OR = 10.6, P = 0.024) as well as < 4 clinic visits (OR = 1.62, P = 0.039) were identified as predictors of undernutrition. Furthermore, the association between malaria and DD was statistically significant (P = 0.015). In this study, undernutrition was highly frequent than malaria infection. Thus, there is an urgent need to improve maternal awareness through nutritional counselling and health campaigns on the benefits of consuming at least five food groups. Besides, improved maternal dietary nutrient intake is likely to have impact on the burden of malaria parasite infection.