In tropical soils, excessive weathering of primary mineral phosphorus (P) has resulted in the depletion of most soluble forms of P, greatly hindering plant productivity. Long-term growth of cover crops in tropical agroforestry systems have been shown to influence P solubility.  We examined several key soil characteristics associated with fertility, emphasizing soil P solubility, after fours years of cover crop establishment.  The experimental design included four leguminous cover crops (Arachis pintoi, Calopogonium mucunoides, Canavalia ensiformis, and Centrosema macrocarpum) and an inorganic fertilizer treatment cultivated in the understory of a cacao agroforestry system in the San Martin district of Peru.  In the 0-5 cm soil horizon A. pintoi significantly increased soil carbon (24.4 g/kg vs. 15.6 g/kg) and soil pH (5.55 vs. 5.18) relative to the control.  In the 5-15 cm soil horizon C. ensiformis significantly increased carbon relative to the control (15.3 g/kg vs. 11.4 g/kg).  In the 0-5 cm depth, ammonium chloride extracted significantly more phosphorus from the fertilized treatment relative to the control treatment (0.65 ug/g vs. 0.14 ug/g). Weak hydrochloric acid extracted significantly less phosphorus from the C. ensiformis (10.31 ug/g), and C. mucunoides (11.5 ug/g) treatments relative to the control treatment (32.89 ug/g).  In conclusion, while four years of cover cropping is long enough to alter soil carbon content and pH, it may not be long enough to alter the most soluble pools of phosphorus.