Herein, we present a greener approach to achieve an ultrasensitive, selective, and viable sensor engineered by amino acids as a recognition layer for simultaneous electrochemical sensing of toxic heavy metals (HMs). Electrochemical techniques like electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), and square-wave anodic stripping voltammetry (SWASV) were applied to demonstrate sensing capabilities of the designed analytical tool. The comparative results of different amino acids demonstrate alanine’s superior performance with a well-resolved and enhanced current signal for target metal ions due to strong complexation of its functional moieties. The working conditions for alanine-modified GCE were optimized by investigating the effect of alanine concentration, different supporting electrolytes, pH values, accumulation potentials, and time. The limits of detection for Zn2+, Cd2+, Cu2+, and Hg2+ were found to be 8.92, 5.77, 3.01, and 5.89 pM, respectively. The alanine-modified electrode revealed absolute discrimination ability, stability, and ultrasensitivity toward metal ions even in the presence of multifold interfering species. Likewise, greener modifier-designed electrodes possessed remarkable electrocatalytic activity, cost affordability, reproducibility, and applicability for picomolar level detection of HM ions in real water sample matrixes. Theoretical calculations for the HM-amino acid interaction also support a significantly improved mediator role of the alanine modifier that is consistent with the experimental findings. © 2019 American Chemical Society.