Chinese plum fruits are rich in phenolic compounds from the flavan-3-ol family, including (+)-catechin and (-)-epicatechin, widely associated with sensory attributes such as bitterness and astringency, beneficial for human health, and involved in enzymatic browning. Leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) enzymes catalyze (+)-catechin and (-)-epicatechin biosynthesis, respectively. It has been described that genes encoding for LAR and ANR are transcriptionally regulated by transcription factors belonging to MYB, bHLH, and bZIP families. In this study, we examined two Chinese plum cultivars (‘98–99’ and ‘Angeleno’) with different flavan-3-ol profiles to characterize MYB transcription factors involved in malus the accumulation of (+)-catechin and (-)-epicatechin in fruits. We observed that fruits of ‘98–99’ accumulate a higher content of (+)-catechin than (-)-epicatechin, while ‘Angeleno’ displays an opposite profile. We identified PsaMYBPA1, PsaMYB7, and a MYB transcription factor not previously described in the literature, which we named PsaMYB700. The expression of PsaMYB700 was up to 10-fold higher in ‘98–99’ than ‘Angeleno’ at the earliest fruit developmental stage. Promoter activation assays indicated that PsaMYBPA1 activates the flavan-3-ol-related genes LAR, anthocyanidin synthase (ANS), and ANR, while PsaMYB7 and PsaMYB700 activate LAR and ANS. In contrast to PsaMYBPA1 and PsaMYB7, PsaMYB700 displays high activation levels without the presence of a bHLH co-regulator. Further, the expression levels of PsaMY700 positively correlate with the higher (+)-catechin accumulation in fruits of ‘98–99,’ compared with ‘Angeleno.’ Finally, we detected a PsabZIP5 with similar expression levels between cultivars, which activates the promoters of PsaMYBPA1, PsaMYB7, and PsaMYB700. This study elucidates the roles of PsaMYBPA1, PsaMYB7, PsaMYB700 and PsabZIP5 in flavan-3-ol biosynthesis, highlighting a hierarchy of transcriptional regulation of these compounds.