Major factors that constrain tropical soil fertility and sustainable agriculture are low nutrient capital, moisture stress, erosion, high P fixation, high acidity with aluminium toxicity, and low soil biodiversity. The fragility of many tropical soils limits food production in annual cropping systems. Because some tropical soils under natural conditions have high biological activity, an increased use of the biological potential of these soils to counter the challenges of food production problems is proposed. Most plant species (including the major crops in the tropics) form beneficial associations with arbuscular mycorrhizal (AM) fungi. These fungi could be the most important and poorly understood resource for nutrient acquisition and plant growth in agriculture. This review treats the role of AM fungi in enhancing physical, chemical, and biological soil quality. It focuses on the roles of AM in maintenance and improvement of soil structure, the uptake of relatively immobile elements, both macronutrients (phosphorus) and micronutrients (zinc), the alleviation of aluminium and manganese toxicity, the interactions with other beneficial soil organisms (nitrogen-fixing rhizobia), and improved protection against pathogens. Mycorrhizal associations enable a better use of sparingly soluble phosphorus pools, thereby increasing the efficiency of added phosphorus fertilizer and of the large relatively immobile phosphorus pools. Mycorrhizal management through agroforestry, reduced soil disturbance or crop rotation, is often a better option than mycorrhizal inoculation, considering the problems and costs of large-scale inoculum production. Research directions that are needed to increase understanding of mycorrhizal associations in tropical cropping systems and to increase mycorrhizal benefit are indicated.