BACKGROUND: The application of controlled postharvest abiotic stresses in carrots induces the production of phenolic compounds, mainly chlorogenic acids, which present diverse biological functions. Aqueous two-phase systems (ATPS) is a liquid-liquid extraction technique that has demonstrated its potential for the fractionation and recovery of bioactive compounds. ATPS have the advantages of using environmentally friendly constituents, ease of scale-up and process integration capability. This experimental work addresses for the first time the recovery of bioactive compounds (mainly hydroxycinnamic acid derivatives) from abiotically stressed carrot tissue using ATPS strategies, including in situ extraction, in alcohol-salt and ionic liquid-salt systems. RESULTS: The partitioning of chlorogenic acid was favored in the ethanol-potassium phosphate system achieving a recovery yield of 81.9%. Hydroxycinnamic acid derivatives fractioning was favored in 1-ethyl-3-methylimidazolium acetate (EMIM-Ac)-potassium phosphate ATPS, where recovery yields up to 85.4% were achieved. The in situ extraction strategy not only demonstrated potential for merging extraction and recovery in the same system but also, depending on ATPS used, allowed differential phenolic profiles to be obtained. CONCLUSION: ATPS strategies (either solid-liquid extraction followed by ATPS or in situ extraction) were shown to have great potential for the recovery of bioactives from stressed carrot tissue. (C) 2014 Society of Chemical Industry