: Micronutrient deficiencies, particularly among pregnant women and children under five years old, remain a significant public health challenge in Nigeria. Despite existing policies and programmes, national data on prevalence and risk factors are fragmented. Objective: To synthesise the current evidence on the prevalence of key micronutrient deficiencies and associated risk factors among pregnant women and children under five years old in Nigeria. : A systematic review and meta-analysis were conducted using peer-reviewed studies that were published between 2008 and 2024. The databases searched included PubMed, Scopus, and African Journals Online. After screening 1207 studies, 37 studies were included: 27 were conducted among pregnant women and 10 were among children. A meta-analysis was conducted to estimate the anaemia prevalence using a random-effects model. A narrative synthesis was conducted to synthesise evidence on other micronutrients (i.e., magnesium, copper, and vitamins C and E) due to the limited data and risk factors. : The pooled prevalence of anaemia was 56% among children and 54% among pregnant women. The prevalence of other micronutrient deficiencies varied widely, with a high prevalence of zinc (86.4%), magnesium (94%), and vitamin D (73.3%) deficiencies in certain regions. The identified risk factors included poor dietary diversity, lower socioeconomic status, low maternal education, infection burden, and early or high parity. Most studies were facility-based and sub-national, limiting the generalisability. : This review highlights a high prevalence of anaemia and micronutrient deficiencies among pregnant women and children in Nigeria. Key risk factors included a poor diet, low maternal education, infections, and reproductive health challenges. Targeted, multisectoral policies are urgently needed to address these gaps and improve health outcomes.