Cyanobacteria in water supplies are considered an emerging threat, as some species produce toxic metabolites, cyanotoxins, of which the most widespread and well-studied are microcystins. Consumption of contaminated water is a common exposure route to cyanotoxins, making the study of cyanobacteria in drinking waters a priority to protect public health. In drinking water treatment plants, pre-oxidation with chlorinated compounds is widely employed to inhibit cyanobacterial growth, although concerns on its efficacy in reducing cyanotoxin content exists. Additionally, the effects of chlorination on abundant but less-studied cyanometabolites (e.g. cyanopeptolins whose toxicity is still unclear) remain poorly investigated. Here, two chlorinated oxidants, sodium hypochlorite (NaClO) and chlorine dioxide (ClO2), were tested on the toxic cyanobacterium Microcystis aeruginosa, evaluating their effect on cell viability, toxin profile and content. Intra- and extracellular microcystins and other cyanometabolites, including their degradation products, were identified using an untargeted LC-HRMS approach. Both oxidants were able to inactivate M. aeruginosa cells at a low dose (0.5 mg L−1), and greatly reduced intracellular toxins content (>90%), regardless of the treatment time (1–3 h). Conversely, a two-fold increase of extracellular toxins after NaClO treatment emerged, suggesting a cellular damage. A novel metabolite named cyanopeptolin-type peptide-1029, was identified based on LC-HRMSn (n = 2, 3) evidence, and it was differently affected by the two oxidants. NaClO led to increase its extracellular concentration from 2 to 80–100 μg L−1, and ClO2 induced the formation of its oxidized derivative, cyanopeptolin-type peptide-1045. In conclusion, pre-oxidation treatments of raw water contaminated by toxic cyanobacteria may lead to increased cyanotoxin concentrations in drinking water and, depending on the chemical agent, its dose and treatment duration, also of oxidized metabolites. Since the effects of such metabolites on human health remain unknown, this issue should be handled with extreme caution by water security agencies involved in drinking water management.