Phenolic compounds, their inhibitory activity against fungal amylase and the occurrence of aflatoxins were determined in edible beans. The free, conjugated and bounded phenolic compounds and their phenolic acid profiles were determined in ten bean varieties. A method for aflatoxin B₁, B₂, G₁ and G₂ determination and confirmation by LC–MS/MS was validated. The red and carioca beans presented the highest total phenolic content (1.8 and 1.2 mg.g⁻¹, respectively); the fradinho and white beans the lowest (0.18 and 0.19 mg.g⁻¹, respectively). In the free and conjugated forms, chlorogenic acid was present in 60% of the samples, while in the bounded phenolic, ferulic acid was in 90% of the samples. The phenolic extracts were able to inhibit fungal amylase, and the PCA analysis confirmed that the relation between the chlorogenic and gallic acids is important to this effect. The absence of aflatoxins in samples confirm the protector effects of these phenolic compounds.