Nationally representative data on the micronutrient status of Ghanaian women and children are very scarce. We aimed to document the current national prevalence of micronutrient deficiencies, anemia, malaria, inflammation, α-thalassemia, sickle cell disease and trait, and under- and over-nutrition in Ghana. In 2017, a two-stage cross-sectional design was applied to enroll pre-school children (6–59 months) and non-pregnant women (15–49 years) from three strata in Ghana: Northern, Middle and Southern Belt. Household and individual questionnaire data were collected along with blood samples. In total, 2123 households completed the household interviews, 1165 children and 973 women provided blood samples. Nationally, 35.6% (95%CI: 31.7,39.6) of children had anemia, 21.5% (18.4,25.0) had iron deficiency, 12.2% (10.1,14.7) had iron deficiency anemia, and 20.8% (18.1,23.9) had vitamin A deficiency; 20.3%(15.2,26.6) tested positive for malaria, 13.9% (11.1,17.3) for sickle trait plus disease, and 30.7% (27.5,34.2) for α-thalassemia. Anemia and micronutrient deficiencies were more prevalent in rural areas, poor households and in the Northern Belt. Stunting and wasting affected 21.4% (18.0,25.2) and 7.0% (5.1,9.5) of children, respectively. Stunting was more common in rural areas and in poor households. Among non-pregnant women, 21.7% (18.7,25.1) were anemic, 13.7% (11.2,16.6) iron deficient, 8.9% (6.7,11.7) had iron deficiency anemia, and 1.5% (0.8,2.9) were vitamin A deficient, 53.8% (47.6,60.0) were folate deficient, and 6.9% (4.8,9.8) were vitamin B12 deficient. Malaria parasitemia in women [8.4% (5.7,12.2)] was lower than in children, but the prevalence of sickle cell disease or trait and α-thalassemia were similar. Overweight [24.7% (21.0,28.8)] and obesity [14.3% (11.5,17.7)] were more common in wealthier, older, and urban women. Our findings demonstrate that anemia and several micronutrient deficiencies are highly present in Ghana calling for the strengthening of Ghana’s food fortification program while overweight and obesity in women are constantly increasing and need to be addressed urgently through governmental policies and programs.