Flavonoids, with therapeutic potential, often encounter challenges due to poor aqueous solubility, which limits their oral bioavailability and efficacy. Phosphorylation presents a promising solution, yet current chemical methods require protective agents to mitigate side product formation. Here, we developed a coupled bienzymatic system using an ATP-dependent dikinase, flavonoid phosphate synthetase (BsFPS), for selective synthesis of flavonoid monophosphates. This system integrates a class III polyphosphate kinase 2 (PPK2-III) for ATP regeneration from AMP, thereby reducing costly ATP consumption and enhancing economic viability. Through PPK2-III screening, ErPPK was identified as a compatible candidate, facilitating a streamlined one-pot system. Structural analysis revealed that the residue at the equivalent site of Arg75ErPPK influences the binding pocket entry distance and flavonoid derivative inhibition propensity on PPK2-III, confirming the compatibility of ErPPK and providing structural insights for identifying PPK2-III with reduced inhibition likelihood. Further optimization strategies, including balancing Mg2+ and polyphosphate ratios, incorporating Tween surfactants for enhanced substrate solubilization without compromising enzyme stability, and increasing the rate-limiting enzyme amount, significantly elevated the conversion rate. Notably, pH control was crucial due to pH decline caused by BsFPS catalysis. pH-stat conversion achieved a 99.0 % conversion of luteolin, the flavonoid target, within 8 h, yielding up to 21.5 mM (7.9 g/L) luteolin monophosphates with up to 95 % reduction in ATP requirement. This enzymatic phosphorylation approach shows promise for advancing polyphenolic monophosphate bioproduction and transforming their functional applications.