Inflammation and infections such as malaria affect concentrations of many micronutrient biomarkers, and hence estimates of nutritional status. We aimed to assess the relationship between malaria infection and micronutrient biomarker concentrations in pre-school children (PSC), school-age children (SAC) and women of reproductive age (WRA) in Malawi, and to examine the potential role of malaria immunity on the relationship between malaria and micronutrient biomarkers. Data from the 2015/2016 Malawi micronutrient survey were used. The associations between current or recent malaria infection, detected by rapid diagnostic test, and concentration of serum ferritin, soluble transferrin receptor (sTfR), zinc, serum folate, red blood cell (RBC) folate and vitamin B12, were estimated using multivariable linear regression. Factors related to malaria immunity including age, altitude and presence of hemoglobinopathies were examined as effect modifiers. Serum ferritin, sTfR and zinc were adjusted for inflammation using the BRINDA method. Malaria infection was associated with 68% (95% CI 51, 86), 28% (18,40) and 34% (13,45) greater inflammation-adjusted ferritin in PSC, SAC and WRA respectively (p<0.001 for each). In PSC, the positive association was stronger in younger children, in high altitude, and in children who were not carriers of the sickle cell trait. In PSC and SAC, sTfR was elevated (+ 25% (16, 29) and + 15% (9,22) respectively, p<0.001). Serum folate and RBC folate were elevated in WRA with malaria (+ 18% (3,35) and + 11% (1,23), p=0.01 and p=0.003 respectively). Malaria affects the interpretation of micronutrient biomarker concentrations and examining factors related to malaria immunity may be informative.