In this study, the hydrophilic silk thread was changed to a hydrophobic surface by a compact cold atmospheric plasma (CAP) using Ar/C6H14 mixture as the working precursor. To test the hydrophobicity of the treated samples, water repellent examinations were performed and the static water contact angle of 139.62° was obtained. The durability of hydrophobicity was investigated using washing cycles and the aging effect. The color test of the samples was performed in CIELAB color space showing good stability in the silk color. To characterize the morphology of the processed samples, the changes in chemical bonds on the surface, deposited thin layer and redistribution of the atomic content on the surface were performed by atomic force microscopy, X-ray photoelectron spectroscopy, field emission scanning electron microscopy, energy-dispersive spectroscopy and X-map analyses, respectively. The CAP key parameters were investigated by the voltage–current profiles and optical emission spectroscopy. Moreover, the mechanical properties of the processed silk threads such as breaking strength, elongation, and extension were found to be improved. The results of this work could be used in the textile factory to modify the silk threads before or after dyeing, as well as for other fibers like wool and polyesters.