Highly branched metal nanostructures are of great interest for creating highly sensitive sensors of various molecules through the use of surface-enhanced Raman scattering. However, the method of manufacturing such nanostructures is often complex and difficult to reproduce. Herein, we report a simple, one-pot synthesis of flower-like gold nanostructures (AuNFs) in a porous Si/SiO2 matrix for potential surface enhanced Raman spectroscopy (SERS) applications. Templates covered with 500-nm diameter AuNFs with rough coral-like petals were obtained through a simple electroless reduction of gold(III) chloride salt in diluted hydrofluoric acid inside pores in the Si/SiO2 layer, which were obtained by swift heavy ion track technology. Detailed SERS analysis showed that single nanoflowers are capable of enhancing Raman signals and can be used as independent nanosensors. Having a few AuNFs in close proximity to each other enables more “hot spots” to be formed with an even greater increase in signal intensity. Using such substrates, good quality SERS spectra could be achieved for 4-mercaptopyridine at a concentration of 0.5 µM. Finally, we theoretically demonstrate that the AuNFs are characterized by a wide-band plasmonic mode as well as by hot spots in the electromagnetic near-field distribution, which can result in a high enhancement factor for Raman scattering.