In this paper, experimental vibration analyses were carried out on biocomposite materials, both with and without an interleaved natural viscoelastic layer. The composites consisted of an exterior Flax/PLA layer and interleaved rubber layers (TPU) of varying thicknesses and positions. The different configurations were manufactured using advanced 3D printing technology. The experimental tests were performed on beam specimens with different stacking sequences, under a clamped-free configuration, utilizing an impulse technique in flexural vibration. This setup allowed for the precise measurement of the composite’s vibrational behavior under varying conditions. To assess the dynamic properties of the composites, resonance vibration experiments were conducted. These experiments were aimed at determining key dynamic parameters, including natural frequencies and modal loss factors for each bending mode. The influence of the viscoelastic layer’s thickness, number, and positioning was carefully examined to understand its impact on the damping behavior of the composites. The results highlight the significant role that the viscoelastic layer plays in enhancing the damping performance of the materials, demonstrating how variations in layer configuration can lead to improved dynamic behavior. This improvement is primarily due to the energy dissipation properties of the viscoelastic layer, which effectively absorbs and dissipates vibrational energy. This study provides valuable insights for the design and optimization of composite materials with enhanced vibration damping capabilities.