Mustard (Brassica juncea L.) seed meal is good source of protein (28-36%) and phenolic antioxidants like sinapic acid and sinapine. In this work an ultrafiltration-diafiltration-based technique is developed for simultaneous preparation of protein isolate and recovery of phenolic rich fraction from seed meal using a high shear rotating disk membrane module with emphasis on reduced membrane fouling effect. The yield of membrane process found less (31.4% on dry basis) compared to precipitation process (42% on dry basis), but a high purity of protein isolate (96%) with improved functional properties was obtained. The phenolic content in the protein was found to be reduced from 7.23 mg/g of protein to as low as 0.6 mg/g of protein in this process. The phenolic-acid-rich fraction recovered shows about 87.24% radical scavenging and 34.3% chelation capacity per 100 ppm concentration. So, this process can be commercially exploited for protein isolate and phenolic antioxidant-rich product preparation after proper scale up.