Integrated soil fertility management (ISFM) technologies for African smallholders should consider (i) within-farm soil heterogeneity; (ii) long-term dynamics and variability; (iii) manure quality and availability; (iv) access to fertilizers; and (v) competing uses for crop residues. We used the model FIELD (Field-scale resource Interactions, use Efficiencies and Long term soil fertility Development) to explore allocation strategies of manure and fertilizers. Maize response to N fertilizer from 0 to 180 kg N ha-1 (±30 kg P ha-1) distinguished poorly responsive fertile (e.g., grain yields of 4.1-5.3 t ha-1 without P and of 7.5-7.5 t ha-1 with P) from responsive (1.0-4.3 t ha-1 and 2.2-6.6 t ha-1) and poorly responsive infertile fields (0.2-1.0 t ha-1 and 0.5-3.1 t ha-1). Soils receiving manure plus fertilizers for 12 yr retained 1.1 to 1.5 t C ha-1 yr-1 when 70% of the crop residue was left in the field, and 0.4 to 0.7 t C ha-1 yr-1 with 10% left. Degraded fields were not rehabilitated with manures of local quality (e.g., 23-35% C, 0.5-1.2% N, 0.1-0.3% P) applied at realistic rates (3.6 t dm ha-1 yr-1) for 12 yr without fertilizers. Mineral fertilizers are necessary to kick-start soil rehabilitation through hysteretic restoration of biomass productivity and C inputs to the soil.