Metal ions serve as essential cofactors in a large fraction of enzymes, where they stabilize substrates, intermediates, and transition states during catalysis. In several metalloenzymes, metal ions have been observed to adopt multiple spatial positions depending on the catalytic stage; however, the structural principles and functional significance of this relocation remain poorly understood. Here, we present a structural and biochemical analysis of a class II pyruvate aldolase from Achromobacter xylosoxidans (AxADL), which catalyzes the Mg²⁺-dependent condensation of pyruvate and formaldehyde to form 2-keto-4-hydroxybutyrate. Crystal structures of AxADL were determined in the apo, Mg²⁺-bound, and Mg²⁺/pyruvate-bound states. AxADL adopts a canonical TIM-barrel fold and assembles into a hexamer via C-terminal α-helix exchange. The active site contains conserved residues that coordinate the catalytic Mg²⁺ ion and facilitate enolate formation, including a methionine residue positioned adjacent to the metal-binding site. Comparative structural analysis reveals that the Mg²⁺ ion occupies two distinct positions separated by approximately 2.5 Å. Upon substrate binding, the metal ion shifts toward the active center, reorganizing its coordination environment to enable direct interaction with the substrate and to promote formation of the catalytic enolate intermediate. This displacement is partly governed by the steric effects of this methionine residue, and its substitution with leucine results in enhanced catalytic activity. Together, these findings provide structural evidence that controlled Mg²⁺ repositioning is central to AxADL catalysis and highlight steric modulation of Mg²⁺ positioning as an underappreciated factor in the function of related metalloenzymes.