Phosphorus (P) plays an important role in the physiological plant processes; however, in tropical soils, P is one of the most limiting nutrients for crop yield due to its low mobility, determined by the adsorption of this element to the soil. To enhance P-use and P-acquisition efficiency, this research aimed to evaluate the effect of cover crops and mycorrhizal colonization on changing soil P fractions, both organic and inorganic. A complete randomized block design was adopted in a field experiment, with four replications using four cover crops: i) pigeon pea (Cajanus cajan); ii) crotalaria (Crotalaria juncea); iii) millet (Pennisetum glaucum); iv) brachiaria (Brachiaria ruziziensis) and v) fallow, as control. The arbuscular mycorrhizal fungus colonization, the fungal spore density, soil P fractionation, and N, P, and K uptake were assessed. Our results show that cover crops affected the soil P cycling in deeper soil layers. Cover crops may increase arbuscular mycorrhizal inoculum potential for the succeeding crop in rotation or intercropping, when used as a green manure.