Recent evidence suggests that persistence of Helicobacter pylori can be explained, at least in part, by the failure of macrophages to kill bacteria. The fate of type 1 H. pylori strain LC11, which expresses the cag pathogenicity island (PAI) and the vacuolating cytotoxin, and type 2 strain LC20, which lacks both these virulence factors, was determined following infection of the murine macrophage cell line RAW 264.7 or the human macrophage‐like cell line THP‐1. Helicobacter pylori strain LC11 displayed enhanced survival in macrophages in comparison with strain LC20 (4.0 ± 0.2 versus 2.1 ± 0.6 log CFU ml⁻¹, P < 0.01) at 24 h. Phagosomes containing strain LC11 showed reduced co‐localization with LysoTracker Red, higher levels of expression of the early endosome marker EEA1 expression and lower expression of the late endosome/lysosome marker LAMP1 relative to internalized strain LC20, both at 2 h and 24 h. These findings indicate that, in contrast to strain LC20, strain LC11 resides in a compartment with early endosome properties and does not fuse with lysosomes. In addition, phagosomes containing LC11 recruited and retained a higher percentage of TACO (coronin 1) protein in comparison with phagosomes containing strain LC20. Furthermore, IFN‐γ stimulation facilitated maturation of phagosomes containing strain LC11 in association with the release of TACO and a reduction in bacterial survival. We have demonstrated through the use of isogenic cagA‐, cagE‐/picB‐ and vacA‐ mutant strains, that VacA plays a significant role in the interruption of the phagosome maturation. Taken together, these results indicate that, following phagocytosis, H. pylori strains expressing the vacuolating cytotoxin arrest phagosome maturation in association with the retention of TACO.