Background Iron deficiency (ID) and anaemia of inflammation (AI) coexist where infections and nutritional deficiencies are common. The aim of this study was to determine burden of ID, anaemia, inflammation and AI in children in malaria endemic Limbe, Mount Cameroon as well as decipher the contribution of some inflammatory cytokines on the concentration of haemoglobin and ferritin. Methods A total of 520 children aged ≤ 15 years old from the Limbe Health District (LHD) were randomly selected and examined in a cross-sectional study for iron deficiency, anaemia, inflammation and inflammation anaemia. Collected blood samples were used for full blood count and inflammatory marker analyses with the aid of a haemoanalyzer and ELISA machine, respectively. Spearman’s rank correlation analysis was used to determine the correlation between cytokines and haemoglobin while multiple linear regression analysis was used to evaluate the effects of inflammatory cytokines on haemoglobin and ferritin concentrations. Results The overall prevalence of anaemia, ID, IDA, inflammation and AI were respectively, 67.5%, 34.6%, 12.9%, 63.1% and 30.2%. Children aged 12‒15 years (P = 0.001), enrolled from the community (P < 0.001), whose parents are civil servants (P < 0.001), living in a home with 6‒10 occupants (P = 0.016), afebrile (P < 0.001) and malaria negative (P = 0.007) had the highest prevalence of ID while, children ≤ 5 years old (P = 0.001), with a family size of 1‒5 occupants (P = 0.033) had the highest prevalence of AI. Haemoglobin concentration positively correlated with concentrations of IFN-γ (P = < 0.001), TNF-α (0.045) and ferritin (P = < 0.001) while a negative correlation was observed with IL-10 (P = 0.003). In the multiple linear regression analysis only IL-6 significantly (P = 0.030) influenced haemoglobin concentration. Conclusions While IL-6 is of significance in the pathology of anaemia, iron deficiency and anaemia of inflammation are of moderate public health concerns in the Mount Cameroon area. Hence, appropriate intervention against anaemia, ID and AI should be directed at children ≤ 5 years and counterparts > 10 years old that bear the highest burden.