Abstract • 0.12 mmol/L Fe(II) enhanced the total anammox activity and bacterial abundance best. • 0.09 mmol/L Fe(II) led to the best performance on relative anammox activity. • 0.75 mmol/L Fe(II) had an immediate but recoverable inhibition on anammox activity. • More genes but not relative level were expressed at higher Fe(II) concentration. Though there are many literatures studying the effects of iron on anammox process, these studies only focus on the reactor performance and/or the microbial community changes, the detailed effects and mechanisms of Fe(II) on anammox bacterial activity and physiology have not been explored. In this study, four Fe(II) concentrations (0.03, 0.09, 0.12 and 0.75 mmol/L) were employed into the enriched anammox culture. The enhancement and inhibition effects of Fe(II) on anammox process and bacterial physiology were investigated. It was discovered that the anammox process and bacterial growth were enhanced by 0.09 and 0.12 mmol/L Fe(II), in which the 0.12 mmol/L Fe(II) had advantage in stimulating the total anammox activity and bacterial abundance, while 0.09 mmol/L Fe(II) enhanced the relative anammox activity better. The anammox activity could be inhibited by 0.75 mmol/L Fe(II) immediately, while the inhibition was recoverable. Both 0.09 and 0.12 mmol/L Fe(II) induced more genes being expressed, while didn’t show a stimulation on the relative expression level of functional genes. And anammox bacteria showed a stress response to detoxify the Fe inhibition once inhibited by 0.75 mmol/L Fe(II). This study provides more information about physiologic response of anammox bacteria to external influence (enhancement and inhibition), and may also instruct the future application of anammox process in treating various sources of wastewater (containing external disturbances such as heavy metals) and/or different treatment strategies (e.g. from side-stream to main-stream).