This study investigated the occurrence and fate of 1,2,5,6,9,10-hexabromocyclododecane (HBCD) and 1,2-dibromo-4-(1,2-dibromoethyl)cyclohexane (TBECH), two chiral brominated flame retardants (BFRs) with sixteen different stereoisomers, in four Hong Kong wastewater treatment plants (WWTPs) featuring diverse treatment processes during a two-year sampling campaign. More effective HBCD removal was achieved via biodegradation as compared to sludge sorption, whereas both chemically enhanced primary treatment and secondary treatment yielded high TBECH elimination (>90%). α-HBCD (54–75%) predominated in all samples, and its proportions were increased in effluent as compared to influent and sludge. α- and β-TBECH (72.3–84.4% in total) were the predominant TBECH diastereomers, with a proportional shift from the latter to the former diastereomer mostly observed after treatment. More rapid biodegradation and preferential sorption of γ-HBCD as compared to α-HBCD as well as β-TBECH as compared to α-TBECH might account for this changing pattern. This is the first study to report the enantiomer-specific behavior of chiral BFRs in different wastewater treatment processes. A preferential elimination of (+)-α- and (+)-γ-HBCD and E2-β-TBECH (the second enantiomeric elution order) took place consistently after biological treatment, possibly due to enantioselective adsorption and microbial degradation. Our results highlight the importance of conducting enantiospecific analysis for chiral pollutants in wastewater samples.