α-amylases are starch-hydrolytic enzymes with considerable economic value in modern fermentation industry. Regulation of its activity at the molecular level may, therefore, offer an attractive step in controlling the fermentation process. As a metalloenzyme, its catalytic activity is dependent on Ca²⁺. A docking study was conducted using AutoDock 4.2.6 for α-amylases (PDB ID: 3BH4) from Bacillus amyloliquefaciens with a well-known chelating agent ethylenediaminetetraacetic acid (EDTA), both in the presence and absence of Ca²⁺. Binding energy and the interacting amino acids in the protein-ligand interaction were determined. Stability of the protein-ligand complex was evaluated using R-plot through ProCheck. A comparative analysis of the EDTA-interacting amino acids with that of amino acids constituting the Ca²⁺ ion-binding pocket indicate that though EDTA was unable to chelate Ca²⁺, it effectively inhibited the enzyme by binding with Gln(N)-251 and Val(V)-2. The inhibition was independent of the presence or absence of Ca²⁺ ions indicating the potential of EDTA to possibly inhibit both β and γ-amylase enzymes. No significant alteration in conformation and stability of the enzyme was observed during inhibition indicating that it could be revived back to its active state through the photodegradation of EDTA molecules under UV light illumination as illustrated in other scientific studies. Thus EDTA could be used as a regulatory switch in establishing a control over the fermentation reaction.