Low-salt soy sauce (LSS) supports healthier diets but suffers taste defects. Endogenous acid-acyl amino acids (AcAAs), β-citryl-l-glutamate (Cit-Glu) and N-lactoyl-l-phenylalanine (Lac-Phe), may help restore taste. In this study, sensory functions and mechanisms of Cit-Glu and Lac-Phe were examined by sensory evaluation and molecular simulation, and their biosynthesis was traced using strain cultures and enzyme assays. Cit-Glu and Lac-Phe exhibited intrinsic umami thresholds (230 and 380 mg·L-1) and boosted kokumi through strong hydrogen bonds with hTAS1R1/hTAS1R3 and CaSR, while competitive binding to OTOP1 and hTAS2Rs suppressed sourness and bitterness. Co-fermenting of Lactiplantibacillus plantarum with Zygosaccharomyces rouxii produced these AcAAs via glutamate N-acetyltransferase (catalyzing acyl group transfer to Glu) and cytosolic nonspecific dipeptidase (catalyzing reverse hydrolysis). Microbiota intervention plus enzymatic strategies increased Cit-Glu and Lac-Phe to 2.25 and 0.87 mM in LSS, significantly reducing sourness and bitterness and enhancing umami and kokumi. These findings provide a practical strategy to optimize taste in sodium-reduced fermented foods.