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In many tropical soils, excessive weath- ering of primary minerals confounded by intense agricultural production has resulted in the depletion of organic matter and plant available forms of phosphorus (P). Long-term growth of cover crops in tropical agroforestry systems have been shown to influence nutrient cycling, and soil organic matter pools. The objective of this experiment was to assess the affect of 2 years of cover-crop cultivation on organic matter accumulation and P bioavailability using Mehlich I and sequential fractionation methods. The experiment included six treatments in the understory of a cacao-plantain agroforestry system adjacent to lower montane tropical forests of the San Martin district of Eastern Peru. Cacao and plantain formed the primary canopy on otherwise abandoned agricultural land. The treatments consisted of four perennial leguminous cover crops (Arachis pintoi, Calopogonium mucunoides, Canavalia ensiformis, and Centrosema macrocarpum), a non-legume cover crop (Callisia repens), and a control treatment (no cover crop). After only 2 years of cultivation, results suggest that all cover crop species accessed residual P pools in 0-5 cm soil depths as indicated by a decrease in the 0.5 M HCl extractable P pools when compared to control. Additional use of residual P pools by A. pintoi and C. macrocarpum were indicated by significant reduction in the 6.0 M HCl extractable P pool. Relative to control, there was no treatment effect on soil organic matter content; however significant differences occurred between treatments. The C. ensiformis, C. mucunoides and C. repens treatments in 5-15 cm soil depths contained significantly more organic matter than the A. pintoi treatment. In 15-30 cm soil depths the C. ensiformis treatment contains significantly more organic matter than the A. pintoi treatment. Continued research should focus on monitoring the long-term effects of cover crop cultivation on the bioavailability of soil P pools in surface soil horizons, development of organic matter pools and the productivity of the agroforestry species.