We presented a microfluidic chip based CL system to determine L-phenylalanine (L-PA). ► It is based on the enhanced CL signal of luminol–H2O2–Cu2+ in the presence of L-PA. ► It gives high sensitivity with small sample volume and short analytical time. ► It shows good linearity over the L-PA concentration in the range of 1.5–120 nM. ► The method is easily applicable to determine L-PA at low concentration in food.