Agroforestry systems are important, globally affecting 1.2 billion people and covering 0.6 billion hectares. They are often cited for providing ecosystem services, such as augmenting soil fertility via N accumulation and increasing soil C stocks. Improved-fallow slash-and-mulch systems have the potential to do both, while reducing nutrient losses associated with burning. In the absence of burning, these systems also have the potential to grow trees through multiple rotations. This project collected soil, mulch, and biomass data over the course of one 9-year crop-fallow rotation and the first two years of the second rotation. A split-plot design was used to assess the effects of P + K fertilization and inclusion of an N-fixing tree species, Inga edulis, on crop and tree biomass production. Fertilization increased growth and nutrient accumulation during Rotation 1 by an average of 36%, ranging from 11% in Parkia multijuga to 52% in Ceiba pentandra. Residual P + K fertilization improved tree and crop growth 20 months into Rotation 2 by an average of 50%, ranging from 15% in Cedrela odorata to 73% in Schizolobium amazonicum. The improved-fallow slash-and-mulch system increased the rates of secondary succession biomass accumulation (11−15 Mg ha−1 yr−1) by 41–64% compared to natural succession (7–8 Mg ha−1 yr−1). Furthermore, P + K fertilization increased secondary-succession biomass accumulation by 9–24%. Nutrient accumulation through biomass production was adequate to replace nutrients exported via crop root and timber stem harvests.