Green membrane separation processes, such as nanofiltration (NF) are promising alternatives for the selective purification of bioactive molecules from pretreated liquid extracts. The conventional extraction methods (Soxhlet, maceration, hydrodistillation, ultrasonication, high pressure extraction, etc.) are time-consuming, expensive, and have shown a poor extraction selectivity. Membrane technology is a novel alternative to obtain bioactive compounds contained in plant and food matrices. The NF of an Array & aacute;n (Luma apiculata) fruit juice was realized to fractionate and identify natural products mainly phenolic compounds. Three different membranes (DL, NFW, and NDX) were used sequentially (molecular weight cut-offs (MWCO): 150-300, 300-500, and 500-700 Da, respectively). ESI/MS/MS allowed the tentative identification of the target metabolites. The results showed an effective fractionation of the target metabolites according to their particular molecular weights and chemical properties. During the three NF stages carried out, the phenolics quercetin, ferulic acid, gallic acid, epicatechin, catechin, myricetin, chrysin, among others were identified in the treated Array & aacute;n juice. Rejection percentages (RP) reaching up to an 100 % were found for various phenolics. However, lower RP occurred in the cases of ferulic acid (-3.22 +/- 1.46 % (NDX)), syringic acid (-100.00 +/- 0.00 % (NDX)), and cryptochlorogenic acid (88.71 +/- 14.02 % (NFW), 95.96 +/- 3.75 % (NDX)). The quantification of phenolics was performed through UHPLC-ESI/MS/MS. The membrane DL allowed the selective permeation of some amino acids with the MW range of about 300 similar to 100 Da (aspartic acid, valine, proline) creating valuable permeate fractions. The membrane DL generated the most important permeate flux ((DL: 21.64-30.42 L/m(2)h) > (NDX: 17.08-21.65 L/m(2)h) > (NFW: 12.30-16.64 L/m(2)h)). The membrane DL allowed the highest recovery of total compounds in the permeate (22.95 %), followed by the NFW (12.75 %) and NDX membranes (17.61 %). Attractive liquid fractions composed of specific phenolics (ferulic acid, syringic acid, cryptochlorogenic acid) and amino acids (aspartic acid, proline, valine, and asparagine) were identified as the membrane permeates DL, NFW and NDX. Permeate liquid fractions of high interest to the pharmaceutical, food and phytochemicals industries were obtained, and appropriate for further process optimization and future scale up.