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The equol contents of 32 samples of Chinese stinky tofu from different manufacturers in China mainland were determined. The results showed that 15 samples of raw stinky tofu contained substantial amounts of equol (1.16 ± 1.69 mg/100 g, wet basis), in which sample c-4 elicited the highest equol of 6.65 mg/100 g, whereas significantly lower equol contents were found in 17 fried samples (0.15 ± 0.14 mg/100 g, wet basis). A significant strong correlation between equol contents and the amino nitrogen contents (p < 0.01, Pearson correlation coefficient 0.725) was observed which indicated the eqoul content was associated with the fermentation extent. Cooking methods influenced the equol contents. Microwaving and frying tofu rapped with starch paste improved the equol contents, whereas deep frying, stir frying, and stewing had negative effects. The study demonstrated stinky tofu served as a good equol dietary source. Extensive fermentation and delicate cooking approaches were necessary for a high-equol final product.