Shortage of alkalinity is a common problem in treating low carbon/nitrogen (C/N) wastewater and industrial influents. It negatively affects system stability and efficiency, but its positive effects remain unclear. To address this issue, insufficient (R1: 400 mg CaCO3/L) and sufficient alkalinity (R2: 750 mg CaCO3/L) levels were established in our study, where R1 served as the experimental group and R2 as the control group. In the experimental group, alkalinity deficiency deteriorated the nitrification and phosphorus removal process by reducing the abundance of functional microbes (Nitrosomonas, genus ammonia-oxidizing bacteria, AOB, and Dechloromonas, genus polyphosphate-accumulating organisms, PAOs) and genes (hao). At the same time, the alkalinity deficiency enriched slow-growing functional microbes (Candidatus_Competibacter, genus glycogen-accumulating organisms, GAOs) and key genes (nirK, norB, nosZ, acnB, fumA, fumB) increased the content of extracellular polymeric substances (EPS) and the ratio of protein to polysaccharide (PN/PS). By day 113, over 87 % of the particles were larger than 200 μm, and complete granulation was achieved. Microbial energy metabolism further indicated that alkalinity deficiency diverted some energy to non-growth metabolism, thereby enhancing microbial heat generation. Our results highlight an innovative approach, using the setting of insufficient alkalinity conditions to improve heat recovery and address the challenges of WWTPs. These research findings are in favor of wastewater treatment plants seeking to meet multiple sustainable objectives, including improving water quality, saving footprint, and maximizing energy recovery.