This study presents the preparation of hybrid nanofiltration membranes based on poly(1,4-phenylene ether ether sulfone), polyacrylonitrile, poly(vinyl pyrrolidone), and SBA-15 mesoporous silica. Laser treatment of polymeric solutions to enhance the hydrophilicity and performance of membranes was investigated. The membranes’ structure was characterized using scanning electron (SEM) and atomic force (AFM) microscopy and contact angle measurements. The addition of PAN in the casting solution produced significant changes in the membrane structure, from finger-like porous structures to sponge-like porous structures. Increased PAN concentration in the membrane composition enhanced the hydrophilicity of the membrane surface, which also accounted for the improvement in the antifouling capabilities. The permeation of apple pomace extract and the content of polyphenols and flavonoids were used to evaluate the efficacy of the hybrid membranes created. The results showed that the hybrid nanofiltration membranes based on PPEES/PAN/PVP/SBA-15: 15/5/1/1 and 17/3/1/1 exposed to laser for 5 min present a higher rejection coefficient to total polyphenols (78.6 ± 0.7% and 97.8 ± 0.9%, respectively) and flavonoids (28.7 ± 0.2% and 50.3 ± 0.4%, respectively) and are substantially better than a commercial membrane with MWCO 1000 Da or PPEES-PVP-based membrane.