Flavonoids are a broad class of polyphenolic compounds with well-established biological and therapeutic relevance; however, their clinical application is often limited by unfavorable pharmacokinetic properties, including low solubility, poor bioavailability, and extensive metabolism. Enzymatic modification has emerged as a promising strategy to overcome these limitations, enabling regio- and stereoselective structural changes under mild and environmentally sustainable conditions. This study presents a systematic review conducted in accordance with the PRISMA 2020 guidelines, covering studies published between 2015 and 2025 on the enzymatic modification of flavonoids and their effects on physicochemical properties and bioavailability, with emphasis on biological activity and therapeutic potential. The literature search was performed in PubMed, Scopus, and Web of Science, complemented by citation searching and exploratory bioinformatics analysis. Evidence from in vitro, in vivo, and clinical studies indicates that enzymatic modifications such as glycosylation, deglycosylation, acylation, hydroxylation, methylation, and prenylation can improve stability, absorption, and biological activity. Despite promising results in experimental models, clinical evidence remains limited. Overall, enzymatic modification represents a promising strategy for improving flavonoid properties; however, most available evidence is derived from in vitro and in vivo studies, and further well-designed clinical trials are required to confirm their therapeutic potential in humans.