Polymethoxyflavones (PMFs) belong to a subgroup of flavonoids that particularly exist in the peels of citrus fruits. Despite their many health-beneficial biofunctionalities, the lipophilic nature of PMFs limits their water solubility and oral bioavailability. To investigate the effect of the delivery system on the improvement of PMF bioavailibility, a lecithin-based emulsion was formulated for the delivery of two PMF compounds, tangeretin and 5-demethyltangeretin. While the emulsion system improved the digestion kinetics and the total solubilized PMF concentrations in in vitro lipolysis studies, the concentration of 5-demethyltangeretin decreased due to chemical transformation to its permethoxylated counterpart, tangeretin. The emulsifier lecithin used in this emulsion formulation contained a choline headgroup as a labile methyl group donor. The presence of a methyl donor potentially caused the transformation of 5-demethyltangeretin and reduced its anti-cancer-cell-proliferation activities. Moreover, this is the first report in the literature of the transformation from 5-demethyltangeretin to tangeretin in a lecithin-based emulsion during lipolysis, and the mechanism underlying this phenomenon has also been proposed for the first time.