The possibility for simultaneous controlled partition of the biologically active alkaloid S-(+)-glaucine, presented in a crude ionic liquid-aqueous plant extract, and separation of the ionic liquid (IL) employed by means of ionic liquid-based aqueous biphasic systems (IL-ABS) was investigated in this study. The ABS were formed by the addition of inorganic salts with distinct water-structuring properties such as Na2CO3, MgSO4, (NH4)2SO4, and NaH2PO4 to an enriched of glaucine extract of Glaucium flavum Cr. (Papaveraceae). The influence of the salt type and concentration on the phase-forming ability, as well as the pH value on the partition of glaucine between the two phases formed, was comprehensively studied. It was found that the target alkaloid is predominantly transferred into the IL-rich phase, regardless the influential factors. The results obtained were further used as a platform for the development of an improved extractive procedure, ensuring simultaneous glaucine recovery, IL recycling and water removal in a single technological step. Thus, based on the formation of a three-phase system consisting of butyl acetate, IL-rich phase, and salt-rich phase, nearly quantitative recovery of glaucine (>99%), IL recycling (ca. 90%), and water removal (ca. 85%) were achieved by salt-induced separation of the crude plant extract.