Although nitrogen (N) is a limiting factor for food production (FP) in Africa, and African food security is seriously threatened by the phenomenon of soil N depletion, there is a dearth of information that shows the points to focus on throughout the chain of FP and food consumption (FC) in all African countries to minimize N loss while securing food N supply. Food N footprint (NF) is an indicator for tracing the losses of reactive N (Nr) with regard to the FP and FC chain. This is the frst study to calculate the food NF for all African countries under fertilized and unfertilized farms, by calculating two sets of virtual N factors (VNFs; kg Nr released to the environment kg− 1 N in consumed product): one for unfertilized farms (the unfertilized scenario) and one for fertilized farms (the fertilized scenario). The fertilized and unfertilized VNFs were utilized to calculate a weighted average set of VNFs (the combined scenario). From the percentage of farms that utilize N fertilizer, and the N percentage in production that comes from soil depletion, the proportion used for the combined scenario was determined. Soil N depletion factors (SNDFs; kg N taken from the unfertilized soil kg− 1 N in food consumed) were also computed to identify the quantity of N extracted from the soil for food production. We have also provided the changes in N inputs, N outputs, and N use effciency (NUE) for North Africa and Sub-Saharan Africa (SSA) during the last 57 years. The average total N input to croplands increased from 24 and 19 kg N ha− 1 yr− 1 in 1961–1965 to 100 and 42 kg N ha− 1 yr− 1 in 2010–2017 for North Africa and SSA, respectively. The NUE declined from 109% and 67% (1961–1965) to 47% and 63% (2010–2017) for North Africa and SSA, respectively. The total average per-capita food NF was 11 and 5.8 kg N cap− 1 yr− 1 in unfertilized farms; 21 and 14 kg N cap− 1 yr− 1 in fertilized farms; and 19 and 7.5 kg N cap− 1 yr− 1 under the combined scenario for North Africa and SSA, respectively. Vegetable-fruit and beef have the highest SDNFs in Africa. FP in Africa contributes approximately 70% of the total food NF. Therefore, if possible, the best way for Africans to reduce soil N depletion and N emissions is to encourage the production and consumption of livestock and crops products with less VNF and SNDF. However, African people do not have this luxury of choice because of poverty and ignorance. Therefore, African policy-makers must adopt integrated approaches that provide effective tools to control the production of animals and crops in conjunction with the improvement of NUE. Trying to completely change the African agricultural system is impossible, but strategies must be developed to reduce soil depletion in a gradual way, as well as a shift towards low-VNF foods