The paper reports on the features and advantages of horizontally oriented flexible silicon nanowires (SiNWs) substrates for surface-enhanced Raman spectroscopy (SERS) applications. The novel SERS substrates are described in detail considering three main aspects. First, the key synthesis parameters for the flexible nanostructure SERS substrates were optimized. It is shown that fabrication temperature and metal-plating duration significantly influence the flexibility of the SiNWs and, consequently, determine the SERS enhancement. Second, it is demonstrated how the immersion in a liquid followed by drying results in the formation of SiNWs bundles influencing the surface morphology. The morphology changes were described by fractal dimension and lacunar analyses and correlated with the duration of Ag plating and SERS measurements. SERS examination showed the optimal intensity values for SiNWs thickness values of 60–100 nm. That is, when the flexibility of the self-assembly SiNWs allowed hot spots occurrence. Finally, the test with 4-mercaptophenylboronic acid showed excellent SERS performance of the flexible, horizontally oriented SiNWs in comparison with several other commercially available substrates.