Pequi (Caryocar Brasiliense Camb.) is a typical fruit from Brazilian Cerrado, rich in antioxidant compounds, such as carotenoids and phenolic substances. Membrane processes allow concentrating extracts at low temperatures, preserving its functional properties. This work reports the results on the carotenoids and polyphenols concentration from pequi aqueous extract by ultrafiltration and nanofiltration processes, in order to develop a natural product rich in biologically active compounds suitable for functional applications. Experimental assays were performed in a dead-end stirred cell and membrane performance was evaluated in terms of permeate flux and permeate and retentate composition in relation to carotenoids and, phenolic substances content as well as antioxidant capacity. The ultrafiltration and the two different nanofiltration membranes presented rejection coefficients around 98%, 100% and 100% of the carotenoids and 65%, 94% and 97% of phenolic compounds, respectively. Thus, the nanofiltration showed a better performance to recovery the antioxidants compounds of pequi aqueous extract.