The fastidious bacterium Leifsonia xyli subsp. xyli (Lxx) is the causal agent of the ratoon stunting disease whose main symptom is a marked reduction in growth observable in adult plants. Lxx may be regarded as an obligate endophyte that grows to pathogenic levels in plant tissue depending on biotic and abiotic stimuli. Thus, we used 2D-DIGE to compare changes in protein profiles of plants colonized with low and high titers of Lxx. Plantlets naturally infected with Lxx were either mock inoculated (low titer treatment) or inoculated with a suspension of Lxx CTCB07 (high titer treatment). Proteins were extracted 30 and 60 days after inoculation (DAI) from leaf whorls and profiles were compared within treatments over time. Quantitative PCR of plant tissue at 30 and 60 DAI indicated that the bacterial population remained low in the first treatment, whereas in the second it increased tenfold. Thirteen and 68 differentially expressed proteins were uniquely detected in the low and high titer treatments, respectively. Protein identification by MS indicated that, in the first case, they were mainly categorized as involved in stress responses. In the second case, however, proteins were functionally more diverse. Noteworthy were markedly downregulated proteins involved in plant growth such as calreticulin and cyclin, and upregulated proteins involved in hormone reception (ABA and JA) and in responses to osmotic stress. These results are consistent with the main symptom of the disease and indicate that temporal changes in protein expression associated with increased bacterial titers could result from altered hormonal balance.