Lactiplantibacillus plantarum is a versatile lactic acid bacterium (LAB) with broad ecological and metabolic adaptability, contributing to both technological and probiotic functions. The prevalence and functional diversity of locally adapted L. plantarum strains in traditional sourdough fermentations remain poorly understood. This study aimed to characterize ten L. plantarum strains isolated from traditional Estonian rye sourdoughs, focusing on safety, enzymatic and carbohydrate metabolism, fermentation performance, exopolysaccharide (EPS) production, and genotype-associated functional diversity, including interaction with aflatoxin B₁ (AFB₁). Strains were γ-hemolytic and susceptible to major antibiotics. Strong aminopeptidase and β-glucosidase activities were observed, whereas α-glucosidase and α-galactosidase activities varied among strains and genotypes. Strains efficiently utilized mono- and disaccharides, with genotype-specific patterns for complex carbohydrates. During sourdough fermentation, all strains acidified the dough (pH < 4.5) and produced lactic and acetic acids in optimal ratios, while fermentation kinetics differed in a genotype-dependent manner. EPS yields (131–225 mg/L) were stable across genotypes. All strains retained fermentative activity in the presence of AFB₁ and exhibited high binding capacity (~100%). These findings demonstrate the safety, metabolic versatility, and genotype-structured functional diversity of L. plantarum from traditional Estonian rye sourdoughs, supporting their application as robust, multifunctional starter cultures for sustainable food fermentations.