The stereoselective biotransformation of methamphetamine (METH), as a chiral compound, during biological treatment in wastewater treatment plants (WWTPs) is often ignored. In this study, a non-racemic form of METH was detected in the raw influent of a full-scale WWTP, with S-(+)-METH as the predominant enantiomer. Stereoselective biotransformation of METH in favor of S-(+)-METH occurred in anaerobic/anoxic and aerobic processes, resulting in the detection of R-(-)-METH as the only enantiomer in the secondary sedimentation tank. To evaluate the stereoselective biotransformation of METH in an activated sludge system, controlled laboratory experiments were conducted under aerobic and anaerobic conditions. Different stereoselective enrichment was observed in a racemic METH batch experiment at various initial concentrations. Batch experiment results with different initial concentrations of nutrient substances demonstrated that the biotransformation of S-(+)-METH occurred simultaneously with the biodegradation of COD and NH4+-N, proving its cometabolism nature. Enzymes released under microbial starvation stress likely stimulated R-(-)-METH biotransformation. Compared with the biotransformation rate of METH under the anaerobic condition, the presence of dissolved oxygen led to a higher biotransformation rate of METH under the aerobic condition.