A systematic review was conducted to evaluate the status and intake of iron, vitamin A, iodine, folate and zinc in women of reproductive age (WRA) (≥15–49 years) and pregnant women (PW) in Ethiopia, Kenya, Nigeria and South Africa. National and subnational data published between 2005 and 2015 were searched via Medline, Scopus and national public health websites. Per micronutrient, relevant data were pooled into an average prevalence of deficiency, weighted by sample size (WAVG). Inadequate intakes were estimated from mean (SD) intakes. This review included 65 surveys and studies from Ethiopia (21), Kenya (11), Nigeria (21) and South Africa (12). In WRA, WAVG prevalence of anaemia ranged from 18–51%, iron deficiency 9–18%, and iron deficiency anaemia at 10%. In PW, the prevalence was higher, and ranged from 32–62%, 19–61%, and 9–47%, respectively. In WRA, prevalence of vitamin A, iodine, zinc and folate deficiencies ranged from 4–22%, 22–55%, 34% and 46%, while in PW these ranged from 21–48%, 87%, 46–76% and 3–12% respectively. Inadequate intakes of these micronutrients are high and corresponded with the prevalence figures. Our findings indicate that nationally representative data are needed to guide the development of nutrition interventions and public health programs, such as dietary diversification, micronutrient fortification and supplementation.