Plant-based alternatives are considered microbiologically safe; however, recent studies have raised concerns about hygienic quality. Additionally, the relationship between microbiological safety and polyphenolic content in fermented products remains unexplored. This study assessed the potential of four autochthonous Lactiplantibacillus plantarum strains (3, 5, 9, and 10) to impact microbial composition and modulate polyphenol and saponin levels in a quinoa-based beverage. The results identified Lactiplantibacillus plantarum strains 3, 9, and 10 as effective in inhibiting Enterobacteriaceae (p = 0.001), and increasing concentrations of glycosylated flavonoids, 3-phenyllactic acid, and saponins. However, Lactiplantibacillus plantarum 10 demonstrated a decrease in saponin levels, whereas Lactiplantibacillus plantarum 5 increased the abundance of aglycones, highlighting strain-specific differences. Notably, principal component analysis revealed less differences between inoculated samples and control, indicating potential contribution of the native microbiota to the fermentation. This study enhances the understanding of interactions between starter cultures, native microbiota, and bioactive compounds in plant-based fermented beverages.