In new food formulations, carotenoids and phenolic compounds are likely to be the most sought after food ingredients according to their bioactivity, nutraceutical, nutritional value, and compatibility properties once incorporated into food formulations. Such solutes are naturally present in many plant-based sources, and some portions are directly consumed when enriching food products and formulations; however, some portions, which are contained in the parts of the plant sources not considered edible, including the leaves, peel, and seeds, among other by-products, are commonly wasted. Related to this, scientists have found a new window for obtaining these bioactive molecules, but their recovery remains a challenge. To some extent, the final purification and polishing requires highly selective performance to guarantee the desired properties and concentration. In this regard, membrane technologies, such as nanofiltration (NF), represent an alternative, owing to their highly selective properties when separating low-molecular-weight compounds. NF becomes immediately suitable when the pretreated extracts are subjected to further efficient concentration, fractionation, and polishing of phenolic fractions and carotenoids. The separation efficiency (usually higher than 97%) of NF technology is high according to the low pore size of NF membranes, but the low temperature in process separation also contributes to the separation of thermolabile compounds. Therefore, this paper reviews the ongoing cases of studies reporting the successful separation and polishing of phenolic fractions and carotenoids from distinct sources. In particular, we have focused our attention on the main interactions during the separation process and the drawbacks and advantages of using membranes for such a case study.