Lactiplantibacillus plantarum is widely used in fermented foods and as a probiotic, yet the genomic basis underlying its γ-aminobutyric acid (GABA) production capacity and strain-level functional diversity remains incompletely resolved. We analyzed 1240 publicly available genomes to map species-wide genome architecture, the distribution of GABA-related genes, and accessory drivers of phenotypes. Pangenome analysis identified 45,201 gene families, including 622 strict core genes (1.38%) and 444 soft-core genes (2.36%). The accessory genome dominated (3138 shell and 40,997 cloud genes; 97.64%), indicating a strongly open pangenome. In contrast, the GABA (gad) operon was universally conserved: gadB (glutamate decarboxylase) and gadC (glutamate/GABA antiporter) were present in all genomes regardless of isolates source. Accessory-genome clustering revealed ecological and geographic structure without loss of the operon, suggesting that phenotypes variability relevant to fermentation and probiotic performance is primarily shaped by accessory modules. Accessory features included carbohydrate uptake and processing islands, bacteriocins and immunity systems, stress- and membrane-associated functions, and plasmid-encoded traits. Analysis of complete genomes confirmed substantial variation in plasmid load (median = 2; range = 0–17), highlighting the role of mobile elements in niche-specific adaptation. Carbohydrate-Active Enzymes database (CAZy) and biosynthetic gene cluster (BGC) profiling revealed a conserved enzymatic and metabolic backbone complemented by rare lineage-specific functions. Collectively, these results position L. plantarum as a genetically stable GABA producer with extensive accessory-encoded flexibility and provide a framework for rational strain selection.