Femtosecond (fs) laser-induced periodic surface structures (LIPSS) were selectively generated on the surface of an Ag-Si alloy consisting of a metallic and a semiconducting phase. For this purpose, the alloy was irradiated with linearly polarized fs-laser pulses (τ = 300 fs, λ = 1025 nm, frep = 100 kHz) using a laser peak fluence F = 0.30 J/cm2. Due to the different light absorption behaviors of the semiconductor (Si) and the metal (Ag) phases that result in different ablation thresholds of the respective phases, pronounced LIPSS with a period of Λ ≈ 950 nm and a modulation depth of h ≈ 220 nm were generated solely on the Si phase. The alloy surface was characterized by scanning electron microscopy, optical microscopy, white-light interference microscopy, and atomic force microscopy before and after laser irradiation. The chemical analysis was carried out by energy-dispersive X-ray spectroscopy, revealing surface oxidation of the Si phase and no laser-induced chemical modification of the Ag phase. The surface wettability of the alloy was evaluated with distilled water and compared to those of the single constituents of the composites. After fs-laser irradiation, the surface is characterized by a reduced hydrophilic water contact angle. Furthermore, the alloy selectively structured with LIPSS revealed a droplet shape change due to the distinctly different contact angles on the Si (θ = 5°) and Ag (θ = 74°) phases. This phenomenon was evaluated and discussed by local contact angle analyses using a confocal laser scanning microscope and Rhodamine B dye. In addition, it was shown that the shape change due to different contact angles of the components allowed a targeted droplet movement on a macroscopic material boundary (Ag/Si) of the alloy. Selectively structured metal/semiconductor surfaces might be of particular interest for microfluidic devices with a directional droplet movement and for the fundamental research of wettability.