To meet the growing interest in the development of innovative biological nutrient removal (BNR) alternatives for energy neutrality, resource recovery, and decarbonization, the adsorption/bio-oxidation (A/B) process has been widely studied for carbon capture and shortcut nitrogen (N) removal, while limited research has focused on incorporating enhanced biological phosphorus (P) removal (EBPR), mainly due to the differential carbon usage characteristics of functionally relevant microorganisms. Here, a full-scale pilot testing with an integrated system combining A-stage high-rate activated sludge (HRAS) with B-stage partial (de)nitrification/anammox and side-stream EBPR (HRAS-P(D)N/A-S2EBPR) was conducted treating real municipal wastewater. The results demonstrated that, despite the low influent carbon load, the B-stage P(D)N-S2EBPR system achieved effective and stable P removal performance, especially when the volatile fatty acid (VFA) load from A-stage was elevated. Sludge fermentation in both A-stage and B-stage promoted carbon redistribution and likely provided more competitive advantages for ammonium-oxidizing bacteria and polyphosphate accumulating organisms, leading to carbon-efficient shortcut N removal mainly through partial nitrification pathway and influent carbon-independent EBPR simultaneously. Exposure to high VFA levels was considered a potential selection factor for the suppression of nitrite-oxidizing bacteria in the system. The involvement of internal carbon-accumulating organisms would potentially play an important role in endogenous denitrification. This study provided new insights into the effects of incorporating side-stream EBPR into the A/B process on microbial ecology, metabolic activities, and system performance.