This study aimed to determine the regulatory role of polyamine–plant growth regulator (PGR) interactions on shoot development and caffeic acid derivatives (CADs) in in vitro shoot cultures of Echinacea purpurea and Echinacea pallida. Nodal explants were cultured under cytokinin-based (0.5 and 1.0 mg/L BAP) and auxin-containing (0.1 mg/L NAA) PGR combinations, supplemented with putrescine or spermidine at 50 and 100 mg/L. Shoot induction rate, number of shoots per explant, total phenolic content (TPC), total flavonoid content (TFC), total antioxidant capacity (TAC), and the contents of caffeic acid derivatives (caftaric acid, chlorogenic acid, caffeic acid, cichoric acid, and echinacoside) were quantitatively determined. The results revealed that shoot induction in both species was not statistically significant with respect to the PGR × polyamine interaction, and that shoot formation was primarily governed by the PGR composition. In contrast, pronounced species-specific differences were observed in secondary metabolism. In E. purpurea, overall phenolic and antioxidant indices remained relatively stable, whereas putrescine application, particularly under 0.5 mg/L BAP, induced a marked compositional redistribution of CADs, with maximum levels of cichoric acid (41.60 mg/g DW), chlorogenic acid (6.51 mg/g DW), and caffeic acid (0.23 mg/g DW). Conversely, E. pallida exhibited higher metabolic plasticity and responded more consistently to spermidine under auxin-containing media, where spermidine maximized chlorogenic acid (4.87 mg/g DW) and echinacoside (1.65 mg/g DW) accumulation alongside coordinated increases in TPC, TFC, and TAC. Overall, the results indicate that the polyamine-mediated modulation of caffeic acid derivatives in Echinacea species is strongly species- and hormone-dependent, underscoring the requirement for species-specific and PGR-conditioned optimization strategies in in vitro shoot culture systems.