Despite intense research in the field of aqueous organic redox flow batteries, low molecular stability of electroactive compounds limits further commercialization. Additionally, currently used methods typically cannot differentiate between individual capacity fade mechanisms, such as degradation of electroactive compound and its cross-over through the membrane. We present a more complex method for in situ evaluation of (electro)chemical stability of electrolytes using a flow electrolyser and a double half-cell including permeation measurements of electrolyte cross-over through a membrane by a UV–VIS spectrometer. The method is employed to study (electro)chemical stability of acidic negolyte based on an anthraquinone sulfonation mixture containing mainly 2,6- and 2,7-anthraquinone disulfonic acid isomers, which can be directly used as an RFB negolyte. The effect of electrolyte state of charge (SoC), current load and operating temperature on electrolyte stability is tested. The results show enhanced capacity decay for fully charged electrolyte (0.9 and 2.45% per day at 20 °C and 40 °C, respectively) while very good stability is observed at 50% SoC and lower, even at 40 °C and under current load (0.02% per day). HPLC analysis conformed deep degradation of AQ derivatives connected with the loss of aromaticity. The developed method can be adopted for stability evaluation of electrolytes of various organic and inorganic RFB chemistries.