Abstract Background Iron deficiency (ID) and micronutrient deficiencies (MNDs) remain significant public health concerns among children. ID is a common diagnosis in pediatric practice; however, other accompanied MNDs may be overlooked. Here, we aimed to determine MNDs accompanying ID and iron deficiency anemia (IDA) in children. Methods This prospective single‐center study included 157 children (6 months–18 years of age) who were referred to the outpatient pediatrics clinic with a possible diagnosis of ID and IDA. Results Of 157 children, 76 (48%) were found to have ID and 27 (17%) had IDA. Vitamin B12, folic acid, copper, zinc, selenium, cobalt, molybdenum, and vitamin A, D, and E levels were compared in 69 children with ID and 69 without ID. Zinc values of children with ID were significantly lower than those without ID ( p = 0.020). The proportion of zinc‐deficient children (21.1%) was significantly higher in children with ID compared with the iron non‐deficient group ( p < 0.001). When children with IDA were compared to children without IDA, children with IDA were 15.36 times more at risk for folic acid deficiency than children without IDA ( p = 0.018) and had significantly lower folic acid levels ( p = 0.005). Children with IDA were 11.39 times more at risk for zinc acid deficiency compared to children without IDA ( p < 0.001), and zinc levels were significantly lower in children with IDA ( p < 0.001). Conclusions In conclusion, we showed that apart from iron, children are susceptible to deficiencies in other essential micronutrients, particularly zinc and folate.