Proanthocyanidins (PAs), also known as condensed tannins, are plant natural products that are beneficial for human and livestock health. As one of the largest grown crops in the world, soybean (Glycine max) is widely used as human food and animal feed. Many cultivated soybeans with yellow seed coats lack PAs or anthocyanins, although some soybean cultivars have coloured seed coats that contain these compounds. Here, we analyse the transcriptional control of PA and anthocyanin biosynthesis in soybean. Ectopic expression of the transcription factors (TFs) GmTT2A, GmTT2B, GmMYB5A or R in soybean hairy roots induced the accumulation of PAs (primarily in phloem tissues) or anthocyanins and led to up-regulation of 1775, 856, 1411 and 1766 genes, respectively, several of which encode enzymes involved in PA biosynthesis. The genes regulated by GmTT2A and GmTT2B partially overlapped, suggesting conserved but potentially divergent roles for these two TFs in regulating PA accumulation in soybean. The two key enzymes anthocyanidin reductase and leucoanthocyanidin reductase were differentially upregulated, by GmTT2A/GmTT2B and GmMYB5A, respectively. Transgenic soybean plants overexpressing GmTT2B or MtLAP1 (a proven up-regulator of the upstream reactions for production of precursors for PA biosynthesis in legumes) showed increased accumulation of PAs and anthocyanins, respectively, associated with transcriptional reprogramming paralleling the RNA-seq data collected in soybean hairy roots. Collectively, our results show that engineered PA biosynthesis in soybean exhibits qualitative and spatial differences from the better-studied model systems Arabidopsis thaliana and Medicago truncatula, and suggest targets for engineering PAs in soybean plants.