Red-fleshed fruits are valued for their vibrant color and high anthocyanin content. Pre-harvest fruit bagging enhances fruit peel pigmentation, but its effect on flesh coloration remains poorly characterized. This study revealed that removing bags from ‘Gengcunyangtao’ red-fleshed peach fruits triggers the rapid and uniform accumulation of anthocyanins in the flesh, resulting in anthocyanin levels that exceed those in unbagged fruits. The exposure to light after bag removal triggered significant increases in anthocyanin levels within 24 h. This was accompanied by the rapid upregulation of light-responsive and flavonoid biosynthetic gene expression levels within 6 h. A metabolomic analysis indicated that anthocyanin precursors, especially p-coumaric acid, accumulated before bag removal, thereby increasing substrate availability for rapid anthocyanin synthesis. On the basis of a weighted gene co-expression network analysis, MYB transcription factors, anthocyanin transporters, glutathione S-transferase, and multidrug and toxic compound extrusion (MATE) were identified as key regulators that coordinate precursor storage along with light-induced transcriptional activation. Notably, PpMYB4 binds to the promoter of PpGSTF14 and activates its expression, thereby promoting anthocyanin accumulation. The study findings elucidated the temporal coordination of metabolic priming and light-responsive transcriptional regulation driving rapid anthocyanin biosynthesis, with possible implications for improving peach fruit flesh coloration.