Biotic interactions in the rhizosphere are biologically important, and although many of those interactions have been well studied, the role of secreted proteins in the cross-talk between microbes and roots has not been investigated. Here, protein secretion was studied during the communication between the roots of two plants (Medicago sativa and Arabidopsis thaliana) and the bacterial symbiont of one of these species (Sinorhizobium meliloti strain Rm1021) and an opportunistic bacterial pathogen of A. thaliana (Pseudomonas syringae pv. tomato DC3000) using a proteomic approach. It was found that protein exudation in the M. sativa-S. meliloti interaction caused an increase in the secretion of seven plant proteins, such as hydrolases, peptidases, and peroxidases among others in two or more time points compared with the plant control. In addition, four proteins, all of bacterial origin, were increased 1.5-fold more in this interaction compared with S. meliloti alone. However, these proteins were not induced when M. sativa was inoculated with P. syringae DC3000. The interaction between A. thaliana and P. syringae DC3000 highly induced the secretion of several plant proteins related to defense soon after initial contact with P. syringae, but these proteins were not secreted in the incompatible interaction with S. meliloti. The results of this study reveal a specific, protein level cross-talk between roots and microbes. These results suggest that secreted proteins may be a critical component in the process of signaling and recognition that occurs between compatible and incompatible interactions.