Release of persistent and potentially toxic per- and polyfluoroalkyl substances (PFAS) and other halogenated compounds into the aqueous environment is an emerging issue and advanced treatment methods are needed for their removal from contaminated water. Destructive treatment methods for PFAS exist, but there is a risk of incomplete degradation, resulting in creation of transformation products during treatment. This study assessed the potential of electrochemical oxidation (EO) for destruction of PFAS and other halogenated compounds, and their transformation products. Suspect and non-target screening were used to explore the chemical space of these samples and identify compounds present before and after the treatment, including transformation products. In total, 21 PFAS classes and 53 individual PFAS were identified using suspect and non-target screening, with confidence level (CL) 3d or higher. Two new classes of PFAS (FASHN and MeOH-FASA) were discovered for the first time. Suspect screening of PFAS revealed that hydro-substituted and ether PFAS could be formed during EO. A total of 12 chlorinated and two brominated compounds were also detected and confirmed with CL 1–3, with six compounds determined to be transformation products. Formation of ammonium oxidation byproducts was hypothesized as being responsible for most identified transformation products formed during EO.