Arbuscular mycorrhizal (AM) fungi are soil-borne microorganisms forming mutualistic associations with the vast majority of land plants, including most agricultural relevant crops. In this association the plant provides the fungus with plant photosynthates allowing it to complete its life cycle, while the fungus provides the plant with mineral nutrients, mainly phosphorus and can also help the plant to tolerate biotic and abiotic stresses. In regard to these benefits there is growing interest on the use of AM fungi to improve productivity and sustainability in agricultural systems. AM fungi and their interactions with plants have been extensively studied using proteomic techniques, but some difficulties have been faced. 1) Little is known about the AM fungal typical protein repertoire because it is currently impossible to grow AM fungi in pure axenic cultures; 2) Plant tissues often contain high amounts of interfering substances that make protein extraction for the study of AM interactions a difficult procedure; 3) Most nutrient exchanges between AM fungi and their host plants involve participation of membrane proteins, still poorly resolved in most separation techniques. Finally, 4) the formation of the arbuscule is an asynchronous process, making it difficult to distinguish which proteins are essential in the early or late stages of AM associations. In this review we present a historical summary of how these difficulties have been overcome by technological advances in proteomics and we discuss current and future trends in the study of the proteins involved in AM interactions.