Phagocytosis of Yersinia pseudotuberculosis by macrophages is initiated by interactions between host cell integrin receptors and the bacterial adhesins, invasin and YadA. Two non-receptor protein tyrosine kinases, FAK and Pyk2, have been implicated in this process. In this study, we investigated the mechanisms of activation and functional requirements for these kinases during phagocytosis. A panel of Yersinia strains that differentially express invasin and YadA were used to infect cells in which FAK and/or Pyk2 expression was reduced by RNA interference. Bacterial strains that simultaneously express invasin and YadA activated FAK and Pyk2 signalling pathways that perform non-redundant functions required for Yersinia internalization. In contrast, FAK activation was found to be sufficient for phagocytosis of bacteria expressing invasin alone, and Pyk2 activation was sufficient when YadA was expressed in the absence of invasin. Based on these data, we suggest that the activation states of FAK and Pyk2, as well as the subsequent signalling events that lead to phagocytosis, are differentially regulated through the unique mechanisms of integrin engagement utilized by invasin and YadA. These findings lend insight into the molecular events that control bacterial phagocytosis as well as other integrin-based processes such as cell adhesion and migration.