Evidence has shown that phosphorus (P) deposited in sediments over multiple decades can be released by microbial activities, leading to recurring harmful algal blooms in several lakes. Sediment microbial fuel cells (SMFC) have been identified as an alternative in-situ approach for limiting P release from sediments to overlying water. However, the effects of SMFC on the micro-environment (pH) in vicinity of the electrodes, which could impact the P distribution, have often been ignored. This study successfully established SMFC systems to investigate their influence on P species and spatial distributions in lake sediments. The results showed that pH was relatively stable in the control group (6.8), while in the SMFC group the pH ranged from 4.63 to 8.26 along the sediment-water profile, suggesting that pH was highly affected by the SMFC system. The overlying water P concentration was much lower in the SMFC group (0.05 mg/L) than the control group (0.14 mg/L). However, P concentration in the sediment pore water of the SMFC group increased from 0.018 to 1.090 mg/L with depth. P fractions in the upper 4 cm of the sediments were highly affected by SMFC operation, but P fractions (i.e., NH4Cl-P, BD-P, and OP) in the SMFC group were not significantly correlated with SRP (p > 0.05). There was a strong correlation between the soluble reactive P (SRP) in pore water and pH (r = -0.930, p