Aiming at developing not only cheaper but also biocompatible and sustainable extraction and purification processes for antibiotics, in this work it was evaluated the ability of aqueous two-phase systems (ATPS) composed of polyethylene glycol (PEG) and cholinium-based salts to extract tetracycline from the fermented broth of Streptomyces aureofaciens. Conventional polymer/salt and salt/salt ATPS were also studied for comparison purposes. The novel systems here proposed are able to extract tetracycline directly from the fermentation broth with extraction efficiencies higher than 80%. A tailored extraction ability of these systems can also be achieved, with preferential extractions either for the polymer- or salt-rich phases, and which further depend on the cholinium-based salt employed. The gathered results support the applicability of biocompatible ATPS in the extraction of antibiotics from complex matrices and can be envisaged as valuable platforms to be applied at the industrial level by pharmaceutical companies.