Sidestream sludge treatment approaches have been developed in recent years to achieve mainstream nitrite shunt or partial nitritation, where NOB are selectively inactivated by biocidal factors such as free nitrous acid (FNA) or free ammonium (FA) in a sidestream reactor. The existence of NOB in raw wastewater has been increasingly realized and could pose critical challenge to stable NOB suppressions in those systems. This study, for the first time, evaluated the impact of influent NOB on the NOB suppressions in a mainstream nitrite shunt system achieved through sidestream sludge treatment. An over 500-day sequential batch reactor operation with six experimental phases rigorously demonstrated the negative effects of influent NOB on mainstream NOB control. Continuously seeding of NOB contained in influent stimulated NOB community shifts, leading to different extents of ineffective NOB suppression. The role of primary wastewater treatment in NOB removal from raw wastewater was also investigated. Results suggest primary settling and High Rate Activated Sludge system could remove a large part of NOB contained in raw wastewater. Primary treatment for raw wastewater is necessary for ensuring stable mainstream NOB suppressions.