A new microfluidic chemiluminescence (MF-CL) method for rapidly assaying the total antioxidant capacity (TAC) of apple and pomegranate juices and honey samples was developed. The method exploited the NaHCO3- H2O2-Co2+ CL reaction. It was found that gallic acid (GA), catechin, caffeic acid, ferulic acid and rutin, as selected phenolic antioxidants, could suppress the CL reaction. The linear range and limit of detection of the method for the antioxidants were as follows: 0.5–3 mg L−1 and 0.27 mg L−1 for GA, 0.2–5.0 mg L−1 and 0.17 mg L−1 for catechin, 0.03–2.0 mg L−1 and 0.03 mg L−1 for caffeic acid, 0.3–2.0 mg L−1 and 0.23 mg L−1 for ferulic acid and 0.3–4.0 mg L−1 and 0.15 mg L−1 for rutin. GA was used as the standard, and the TAC of the fruit juices and honey samples as presented as GA equivalents (GAE). MF-CL was compared with DPPH% and Folin–Ciocalteau (FC) methods.