Mycorrhizal fungi play a crucial role in agroecosystems with their ability to enhance nutrient and water uptake and aid in weeds and pest suppression. Mycorrhizal fungi have a symbiotic association with plants, one which is highly influenced by the interaction between soil and plant conditions. In this study, we analyzed the potential to increase the density and diversity of mycorrhizal fungi of using four different cover-crops: lablab (Lablab purpureus), sunn hemp (Crotalaria juncea), pearl millet (Pennisetum glaucum), and sudangrass (Sorghum drummondii). We examined changes in the density, diversity and structure of mycorrhizal fungi before and after planting the cover crops. Our results indicate that, while the diversity of mycorrhizal fungi was not influenced by the cover-crop type, different cover crops were associated with changes in the density and structure of mycorrhizal fungi. In addition, the cover-crop type also had an impact on the soil organic matter and nutrient status. Of the four we tested, sunn hempwas associated with higher rates of percent organic matter, abundance of mycorrhiza spores, and specific micronutrients, signaling multiple benefits as a warm season cover crop, especially in organic farms that aim to minimize chemical applications.