Pequi is a local important Brazilian fruit, which presents substantial phenolic compounds that justify the processing of this fruit. Here we investigated the clarification and concentration of pequi fruit extract by membrane processes. Microfiltration through a membrane of 0.22 mu m was applied to clarify the pequi extract and total solids and lipids were reduced in 50 and 65%, respectively. However, the microfiltered extract still presented a cloudy appearance (turbidity of 649 NTU) and sequential processes (ultra and nanofiltration) were applied for a further clarification and concentration. Sequential ultra and nanofiltrations presented retention factor lower than 45% for total polyphenol compounds. Ultrafiltration was especially efficient in retaining larger molecules (ellagic acid), while the smallest molecule (p-coumaric acid) was retained by the sequential nanofiltration process. Direct ultra and nanofiltration processes presented greater retention factors and yields than the sequential processes. However, the permeate flux in the direct process were lower than in the sequential membrane filtration processes. Thus, sequential membrane filtration processes are recommended to clarify and fractionate pequi fruit extract, while direct ultra and nanofiltrations presented the greatest retention factors and yields for bioactive compounds from pequi extract.