Membrane technology allows the separation of active compounds, providing an alternative to conventional methods such as column chromatography, liquid-liquid extraction, and solid-liquid extraction. The nanofiltration of a Muérdago (Tristerix tetrandus Mart.) fruit juice was realized to recover valuable metabolites using three different membranes (DL, NFW, and NDX (molecular weight cut-offs (MWCOs): 150~300, 300~500, and 500~700 Da, respectively)). The metabolites were identified by ESI-MS/MS. The results showed that the target compounds were effectively fractionated according to their different molecular weights (MWs). The tested membranes showed retention percentages (RPs) of up to 100% for several phenolics. However, lower RPs appeared in the case of coumaric acid (84.51 ± 6.43% (DL), 2.64 ± 2.21% (NFW), 51.95 ± 1.23% (NDX)) and some other phenolics. The RPs observed for the phenolics cryptochlorogenic acid and chlorogenic acid were 99.74 ± 0.21 and 99.91 ± 0.01% (DL membrane), 96.85 ± 0.83 and 99.20 ± 0.05% (NFW membrane), and 92.98 ± 2.34 and 98.65 ± 0.00% (NDX membrane), respectively. The phenolic quantification was realized by UHPLC-ESI-MS/MS. The DL membrane allowed the permeation of amino acids with the MW range of about 300~100 Da (aspartic acid, proline, tryptophan). This membrane allowed the highest permeate flux (22.10-27.73 L/m2h), followed by the membranes NDX (16.44-20.82 L/m2h) and NFW (12.40-14.45 L/m2h). Moreover, the DL membrane allowed the highest recovery of total compounds in the permeate during the concentration process (19.33%), followed by the membranes NFW (16.28%) and NDX (14.02%). Permeate fractions containing phenolics and amino acids were identified in the membrane permeates DL (10 metabolites identified), NFW (13 metabolites identified), and NDX (10 metabolites identified). Particularly, tryptophan was identified only in the DL permeate fractions obtained. Leucine and isoleucine were identified only in the NFW permeate fractions, whereas methionine and arginine were identified only in the NDX ones. Liquid permeates of great interest to the food and pharmaceutical industries were obtained from plant resources and are suitable for future process optimization and scale-up.