The aim of the study was to provide an in-depth characterization of the methanol-aqueous extract from the aerial parts of Gypsophila glomerata Pall. Ex Adams (Caryophyllaceae) (EGG) and to assess its protective potential on carbon tetrachloride (CCl4)-induced liver and kidney damage in male Wistar rats. Twenty-two flavonoid C-, O- and C,O--glycosides in EGG were annotated by mass spectrometry--based molecular networking; nine of them are reported in this species for the first time. Fourteen-day oral administration of EGG at a dose 200 mg kg−1 bm prevented significantly CCl4-induced liver injury, discerned by an amelioration of the markers of oxidative stress (GSH and MDA) and transaminase activity. EGG decreased the serum level of urea and creatinine as well. The observed improvement of biochemical parameters was supported by histopathological observations. The protective hepatorenal effects of EGG, rich in 2“-О-pentosyl-6-С-hexosyl-apigenin/luteolin/ methylluteolin and their acetyl- and methoxycinnamoyl-derivatives, were comparable with the effects of the positive control silymarin.