The current study presents the first nitrogen (N) and phosphorus (P) footprints calculator for Sub-Saharan Africa during 1961–2017 using an adjusted N-Calculator model, by calculating two sets of virtual N factors (VNFs) or virtual P factors (VPFs): one for fertilized farms and one for unfertilized farms. We furthermore calculated the future food footprints of N (NF) and P (PF) under five scenarios include: 1) business as usual [BAU], 2) achieve an equitable diet (EqD) while the plant N and P uptake and all other food losses would be constant at 2017 level [S1], 3) follow the EqD without any changes in plant N and P uptake, but the current ratio of other food losses would increase by 50% [S2], 4) follow the EqD with a 5% less in plant N and P uptake than the current ratio, and the current ratio of other food losses would increase by 50% [S3], and 5) follow the EqD with a 10% greater in plant N and P uptake than the current ratio, while the current ratio of other food losses would decrease by 50% [S4]. NF (kg N cap−1 yr−1) and PF (kg P cap−1 yr−1) increased from 6.7 and 1.1 to 8.3 and 1.5 during 1961–2017, respectively. The national NF (Tg N yr−1) and PF (Tg P yr−1) increased from 1.6 and 0.26 to 7.7 and 1.4, respectively. In 2050, NF would be 9.7, 21.7, 24.1, 27.7, and 15.5 kg N cap−1 yr−1 for the BAU, S1, S2, S3, and S4 scenarios, respectively. While, PF would be 1.8, 5.1, 5.6, 7.3, and 3.0 kg P cap−1 yr−1, respectively. S4 scenario results in much less NF and