Yersinia enterocolitica (Ye) evades the immune system of the host by injection of Yersinia outer proteins (Yops) via a type three secretion system into host cells. In this study, a reporter system comprising a YopE-β-lactamase hybrid protein and a fluorescent staining sensitive to β-lactamase cleavage was used to track Yop injection in cell culture and in an experimental Ye mouse infection model. Experiments with GD25, GD25-β1A, and HeLa cells demonstrated that β1-integrins and RhoGTPases play a role for Yop injection. As demonstrated by infection of splenocyte suspensions in vitro, injection of Yops appears to occur randomly into all types of leukocytes. In contrast, upon infection of mice, Yop injection was detected in 13% of F4/80+, 11% of CD11c+, 7% of CD49b+, 5% of Gr1+ cells, 2.3% of CD19+, and 2.6% of CD3+ cells. Taking the different abundance of these cell types in the spleen into account, the highest total number of Yop-injected cells represents B cells, particularly CD19+CD21+CD23+ follicular B cells, followed by neutrophils, dendritic cells, and macrophages, suggesting a distinct cellular tropism of Ye. Yop-injected B cells displayed a significantly increased expression of CD69 compared to non-Yop-injected B cells, indicating activation of these cells by Ye. Infection of IFN-γR (receptor)- and TNFRp55-deficient mice resulted in increased numbers of Yop-injected spleen cells for yet unknown reasons. The YopE-β-lactamase hybrid protein reporter system provides new insights into the modulation of host cell and immune responses by Ye Yops. An important strategy of Yersinia enterocolitica (Ye) to suppress the immune defense is to inject bacterial proteins (Yersinia outer proteins, Yops) after cell contact directly into host cells, which affects their functions. However, tracking of cells in which Yop injection occurred has only been described for Yersinia pestis thus far. We adapted the described reporter system specifically for the use of infections with Ye and report the usefulness and limitations of this system. Using cell culture experiments, we demonstrated that β1-integrins and the RhoGTPases RhoA and Rac1 are involved in Yop injection. Since cell culture experiments also revealed that Yop injection is detectable in a similar manner into all subpopulations of the spleen, the system can be used to detect interaction of bacteria with host cells in vivo. In a mouse infection model we found that follicular B cells, granulocytes, macrophages, and dendritic cells are the main targets of Yop injection. Interestingly, Yop-injected B cells displayed an increased activation as indicated by increased CD69 expression. In contrast, interaction of bacteria with T cells seems to be rather a rare event. In immunocompromised gene-targeted mice we found increased frequencies of Yop-injected host cells for yet unknown reasons. Taken together, this novel reporter system represents a powerful tool to further study interaction of host cells with Ye.