FAHF-2 has been shown to prevent peanut-induced anaphylaxis in a murine model. Phase I trials have demonstrated that FAHF-2 is a safe treatment for patients with food allergy. To complete the ongoing phase II study of safety and efficacy of FAHF-2, several batches of FAHF-2 were generated. The aim of this study was to analyze the chemical and biological consistency of different batches of FAHF-2 using our established methods. HPLC chromatogram data of each batch of FAHF-2 product were collected for analyzing product consistency. The bioactivities of 3 different batches of FAHF-2 (batch number1106, 0909 and 0202) were analyzed by culturingU266 (human B cell myeloma cell line), RBL-2H3 (mast cell line), and RAW 264.7 (mouse macrophage cell line) in the presence of 31, 62, 125, 250, and 500 μg/ml of FAHF-2. IgE production by U266, β-hexosaminidase release by RBL-2H3, and TNF-α production by RAW 264.7 cells were determined. Untreated cells were used as controls. Three biomarkers, berberine, jatrorrhizine, and ganoderic acid D, were used as indicators of FAHF-2 batch consistency. HPLC chromatogram data showed that batches of FAHF-2 had similar peak intensities of these three biomarkers. The in vitro assays showed that different batches of FAHF-2 all significantly inhibited IgE production by B cells, TNF-α production by macrophage cells, and degranulation by mast cells. IC50 values of 3 batches were comparable in the three bioactivity assays. This study shows that different batches of FAHF-2 used in clinical trials exhibited chemical consistency and biological potency in vitro.