Biosynthetic organic matters, such as humus, play important roles in iron and phosphorus cycling in soil and aquatic systems. As an important member of humus, fulvic acid (FA) is ubiquitous in different environmental media, such as water, soil, and sediments. In this study, we fabricated the network among phosphate supply, metabolism pathway of FA, iron reduction, and vivianite recovery at the batch scale. Both the vivianite recovery performance and the content of biosynthetic FA were positively related to the phosphorus dosage. The highest vivianite formation efficiency of 53% was obtained in the Fe/P = 1 batch, accompanied with the maximal iron reduction rate of 2.29 mM·day-1, which was 2.66 times higher than that of the Fe/P = 3 batch. Simultaneously, the highest content of FA was detected in extracellular polymeric substances (EPS) of the Fe/P = 1 batch. Metabolome analysis revealed that FA biosynthesis was mainly relevant to tricarboxylic acid (TCA) cycle, amino acid metabolism, and purine metabolism, with glutamate and aspartate as the precursors. Sufficient phosphate stimulated the FA biosynthesis by modulating the biosynthesis and transformation of glutamate and aspartate. After adding 10 mg L-1 FA in Fe/P = 1 batch, the maximal iron reduction rate increase by 35%, as well as 12% improvement of the vivianite formation efficiency. Transcriptome revealed that FA promotes iron reduction and vivianite recovery by upregulating the expression of metal ion binding-, flagella-, and electron transfer activity-related genes.