Three-dimensional (3D) printing technology has attracted great attention for prototyping different electrochemical sensor devices. However, chiral recognition remains a crucial challenge for electrochemical sensors with similar physicochemical properties such as enantiomers. In this work, a magnetic covalent organic framework (COF) and bovine serum albumin (BSA) (as the chiral surface) functionalized 3D-printed electrochemical chiral sensor is reported for the first time. The characterization of the chiral biomolecule-COF 3D-printed constructure was performed by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and energy-dispersive X-ray spectroscopy (EDX). A tryptophan (Trp) enantiomer was chosen as the model chiral molecule to estimate the chiral recognition ability of the magnetic COF and BSA-based 3DE (Fe3O4@COF@BSA/3DE). We have demonstrated that the Fe3O4@COF@BSA/3DE exhibited excellent chiral recognition to l-Trp as compared to d-Trp. The chiral protein-COF sensing interface was used to determine the concentration of l-Trp in a racemic mixture of d-Trp and l-Trp. This strategy of on-demand fabrication of 3D-printed protein-COF-modified electrodes opens up new approaches for enantiomer recognition.