The partial nitritation (PN)–anammox (PN/A) process offers a sustainable alternative to nitrogen management in wastewater treatment, addressing the high costs and increasing the low eco-friendliness associated with traditional nitrification/denitrification processes. Stable partial nitritation (PN) is critical for effective PN/A operation, and this study specifically focused on the need to suppress nitrite-oxidizing bacteria (NOB) to facilitate the enrichment of ammonia-oxidizing bacteria (AOB). Utilizing two sequencing batch reactors (SBRs), PN1 and PN2 with different free ammonia (FA) concentrations, this study aimed to evaluate the NOB suppression strategy while enriching AOB. The PN2 reactor, which operated with a higher initial FA concentration (50 mg/L), successfully maintained high nitritation activity, with 96.1% ammonium removal efficiency (ARE) and 95.1% nitrite accumulation efficiency (NAE) at reduced influent NH4+-N concentrations (50 mg NH4+-N/L, FA 10 mg/L). In contrast, PN1 showed inadequate NOB suppression due to lower FA concentrations (10 mg/L). These results suggest that initiating the nitritation process with higher FA concentrations can effectively suppress NOB, enhancing the stability and efficiency of PN/A processes in mainstream applications.