Summary Trypanosoma cruzi is the aetiological agent of Chagas' disease, a chronic infection that affects millions in Central and South America. Proteolytic enzymes are involved in the development and progression of this disease and two metallocarboxypeptidases, isolated from T. cruzi CL Brener clone, have recently been characterized: TcMCP‐1 and TcMCP‐2. Although both are cytosolic and closely related in sequence, they display different temporary expression patterns and substrate preferences. TcMCP‐1 removes basic C‐terminal residues, whereas TcMCP‐2 prefers hydrophobic/aromatic residues. Here we report the three‐dimensional structure of TcMCP‐1. It resembles an elongated cowry, with a long, deep, narrow active‐site cleft mimicking the aperture. It has an N‐terminal dimerization subdomain, involved in a homodimeric catalytically active quaternary structure arrangement, and a proteolytic subdomain partitioned by the cleft into an upper and a lower moiety. The cleft accommodates a catalytic metal ion, most likely a cobalt, which is co‐ordinated by residues included in a characteristic zinc‐binding sequence, HEXXH and a downstream glutamate. The structure of TcMCP‐1 shows strong topological similarity with archaeal, bacterial and mammalian metallopeptidases including angiotensin‐converting enzyme, neurolysin and thimet oligopeptidase. A crucial residue for shaping the S1′ pocket in TcMCP‐1, Met‐304, was mutated to the respective residue in TcMCP‐2, an arginine, leading to a TcMCP‐1 variant with TcMCP‐2 specificity. The present studies pave the way for a better understanding of a potential target in Chagas' disease at the molecular level and provide a template for the design of novel therapeutic approaches.