This study discusses the influence of the morphological characteristics of molybdenum disulfide (MoS2) substrates on the detection efficiency of Rhodamine B (RhB) via surface‐enhanced Raman scattering (SERS). Commercially available MoS2 powder and vertically aligned (VA‐MoS2) synthesized using a chemical vapor deposition (CVD) technique are compared. The MoS2 substrates are functionalized with silver nanoparticles Ag(NPs) through DC‐magnetron sputtering employing nitrogen as reactive gas. Scanning electron microscopy is employed to probe the morphology of the Ag‐ functionalized MoS2 powder and VA‐MoS2 samples. Raman spectroscopy demonstrates a significant enhancement in the SERS signal that can be attributed 1) to the MoS2 valence band alteration reinforcing the chemical mechanism and 2) to the enhanced electric field generated by the Ag(NPs). The VA‐MoS2 substrate decorated with Ag(NPs) exhibited a high enhancement factor of 3.5 × 108 and a low limit of detection of 10−12 m. The abundance of platelet edges, enhanced by the vertically aligned shape, offers a higher amount of strong and localized electromagnetic field formed between nanoparticle dimers located on the edges, leading to a pronounced enhancement of the SERS signal.