Aim To investigate macrophage function in the presence of sustained infection with Enterococcus faecalis, a prevalent root canal resident in asymptomatic apical periodontitis. Methodology The human monocyte cell line (THP‐1) was differentiated into macrophages by exposure to phorbol myristate acetate (PMA), and the cultures were inoculated with E. faecalis for up to 48 h. At three time‐points 90 min, 24 and 48 h after inoculation, the macrophages and their supernatants were examined. Assays included macrophage phagocytosis rate and vitality, bacterial survival, reactive oxygen species (ROS) production, mitochondrial activity, cytokine production and the expression of pro/anti‐inflammatory M1/M2 markers. Also, periapical tissue from apicectomy samples of human endodontically treated teeth were collected for histological and immunofluorescent analysis. Statistical differences were analysed with RM ANOVA. Results E. faecalis were phagocytized, and subsequently, most of the macrophages underwent apoptosis and necrosis. The small population of macrophages that remained vital after 48 h post‐inoculation harboured surviving bacteria. Despite a reduction in the number of macrophages over time, the mitochondrial activity of the surviving macrophages remained constant and external ROS decreased, whereas internal ROS increased. During the infection, a shift to a M2 macrophage population at 48 h post‐infection was observed; the results were similar to those obtained in periapical human tissue biopsies (p < .05). Conclusions The study portrays a continuous non‐resolved infection with E. faecalis and activation of macrophages that are polarized to the M2 pro‐resolution phenotype.