Nejayote is recognized as the main by-product resulting from the nixtamalization process of maize kernels, which is categorized as an alkaline residue with a chemical composition based on carbohydrates (37.8–55.7%), fiber (22.8–25.5%), protein (4.9–7.4%), and lipids (0.4–1.5%). In addition, Nejayote has an extensive content of simple (e.g., phenolic acids) and complex phenolic compounds (e.g., anthocyanins), which are responsible for the pigmentation and antioxidant activity of maize; therefore, there is a need of their identification depending on the type of maize. The current research has focused on the efficient extraction and identification of the phenolic acids contained in Nejayote after the processing of different types of maize. The target of this work was to fractionate Nejayote from white (NWM), red (NRM), and purple maize (NPM), using three different membranes, such as microfiltration (MF with a pore size of 1 μm) and ultrafiltration (UF100 and UF1 with a molecular weight cut-off of 100 kDa and 1 kDa, respectively), which were strategically applied to extract phenolic acids while retaining other molecules. Such a membrane system exhibited a retention in the first stage of almost all carbohydrates (MF-Retentate: ca. 12–19 g GE/L), while second stage (UF100-Permeate) a concentration of phenolic components was recovered ranging from 768 to 800 mg GAE/L. Finally, in the third stage (UF1-Permeate), 14 phenolic acids were identified, including ferulic and
p-
coumaric acids, derived from caffeic and ferulic acids, along with other molecules (e.g., glucose and fructose).