In this study the environmental fate of two novel trifluoromethoxy-substituted surfactants with respectively an ether or thioether linkage were investigated, of which the design aimed for less persistency and complete mineralization. Long-term microbial transformation studies under aerobic conditions in activated sludge-wastewater medium were performed for 126 days. A semi-closed experimental system with a trapping sorbent was selected to avoid losses of possible volatile transformation products (TPs). The changes in the concentration of the surfactants and their expected TPs were monitored by target analysis using liquid chromatography–tandem mass spectrometry. Significant decrease in the concentration of the surfactants was observed over the incubation period. The main detected TPs were short-chained carboxylic acids (CAs), including a CA with two fluorinated carbon atoms representing the last product prior to mineralization. High stability of these CAs and lack in the formation of inorganic fluoride over the incubation time was however observed. Consequently, unequivocal final mineralization of the investigated surfactants could not be confirmed. Regarding the mass balance, the total amount of detected substances achieved only 30–37% of the expected concentration at the end of the incubation time. The reason of the incomplete mass balance should be further investigated.