During flight, vibrations potentially cause aerodynamic instability and noise. Besides muscle control, the intrinsic damping in bird feathers helps to reduce vibrations. The vanes of the feathers play a key role in flight, and they support feathers’ aerodynamic function through their interlocked barbules. However, the exact mechanisms that determine the damping properties of the vanes remain elusive. Our aim was to understand how the structure of the vanes on a microscopic level influences their damping properties. For this purpose, scanning electron microscopy (SEM) was used to explore the vane’s microstructure. High-speed videography (HSV) was used to record and analyze vibrations of feathers with zipped and unzipped vanes upon step deflections parallel or perpendicular to the vane plane. The results indicate that the zipped vanes have higher damping ratios. The planar surface of the barbs in zipped vanes is responsible for aerodynamic damping, contributing 20%–50% to the whole damping in a feather. To investigate other than aerodynamic damping mechanisms, the structural and material damping, experiments in vacuum were performed. High damping ratios were observed in the zipped vanes, even in vacuum, because of the structural damping. The following structural properties might be responsible for high damping in feathers: (i) the intact planar surface, (ii) the interlocking of barbules, and (iii) the foamy inner material of the barb’s medulla. Structural damping is another factor demonstrating 3.3 times (at vertical deflection) and 2.3 times (at horizontal deflection) difference in damping ratio between zipped and unzipped feathers in vacuum. The shaft and barbs filled with gradient foam are thought to increase the damping in the feather further.