The surface modification of cellulose fibres was performed with the use of low-pressure water vapour plasma, followed by the application of a pad-dry-cure sol-gel coating with the water- and oil-repellent organic-inorganic hybrid precursor fluoroalkyl-functional siloxane (FAS), with the aim of creating the “lotus effect” on the cotton fabric surface. The tailored “lotus effect” was confirmed by measurements of the contact angle of water (154°) and n-hexadecane (140°), as well as by measurements of the water sliding angle (7°), which were used to identify the super-hydrophobic, oleophobic and self-cleaning properties of the modified fibres. The chemical and morphological changes caused by modifications of the fibres were investigated by XPS, FTIR, AFM and SEM. The results show that the plasma pre-treatment simultaneously increased the surface polarity, average roughness, and surface area of the fabric. The application of the FAS coating after plasma pre-treatment caused only a slight increase in the surface roughness, accompanied by a decrease in the surface area, indicating that the architecture of the surface was significantly changed. This result suggests that the surface pattern affected the “lotus effect” more than the average surface roughness. The plasma pre-treatment increased the effective concentration of the FAS network on the fabric, which resulted in enhanced repellency before and after repetitive washing, compared with that of the FAS-coated fabric sample without the plasma pre-treatment. Despite the fact that the plasma pre-treatment increased the concentration of the oxygen-containing functional groups on the fabric surface, this phenomenon insignificantly contributed to the adhesion ability and, consequently, the washing fastness of the FAS coating.