The research on the isolation and recovery of added-value products from biomass has been a hot topic of research in the framework of the biorefinery, aiming a sustainable conversion of biomass into energy, fuels and chemicals. However, the use of the biomass potential is still restricted by the lack of cost-effective processes. In the past decade, ionic liquids (ILs) have been largely investigated as alternative solvents for the extraction and purification of added-value compounds, such as alkaloids, flavonoids, terpenoids and lipids, among others, present in natural sources. Although several works have been published highlighting the potential of ILs as alternative solvents, the isolation/purification of the target compounds as well as the recovery of the solvents for further use has been seldom studied. This chapter presents an overview on the use of supported ILs onto silica or polymers and on IL-based aqueous biphasic systems (ABS) for the purification of high-value compounds present in natural matrices is outlined. The recovery procedures applied to ILs envisaging their recyclability are also presented and discussed. Only after the development of suitable and integrated methodologies, either for the added-value products or ILs recovery, can these be applied in a large scale under the biorefinery framework while decreasing the cost and the environmental footprint of the whole process.