The 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay is commonly applied for appraising antioxidant activity of plant extracts. To test the potential interference of borate on DPPH assay, the effects of borates (0–16 mM sodium tetraborate) on the DPPH radical scavenging ability of gallic acid (GA, at 10, 20 and 40 mg/L) were studied. The presence of borate led to a remarkable reduction of DPPH inhibition of GA, and its DPPH radical scavenging ability can be suppressed contingently on borate content. This interference was interpreted to be resulted from the autoxidation of GA as well as the formation of GA-borate ester complex under alkaline pH (~9.50) of borate. Natural polyphenol extracts from apple peels, parsley and lettuce leaves (as boron-enriched representatives) also exhibited a reduced ability in eliminating DPPH radicals when spiked with borates. In order to avoid this limitation, the utilization of acetate buffer at pH 5.50 for sample preparation is proposed. This work pointed to the possible underestimation of antioxidant properties of polyphenol extracts originated especially from boron-enriched or borate pretreated plants by DPPH assay.