Herein, a silver-chitosan nanocomposite for application in surface enhanced Raman spectroscopy (SERS) sensing was proposed. It was shown that optically transparent chitosan coatings with 0.8 μm thickness allow penetration of target analytes to silver nanoparticles and the analysis in both polar and nonpolar solvents. Under the chosen conditions, chitosan formed continuously smooth films and coatings stabilizing rough nanostructured metallic surfaces and served as a suitable matrix for immobilization, uniform spreading, and preconcentration of the analytes. Polycyclic aromatic sulfur heterocycles were chosen as target analytes being one of the most important fuel quality markers, hazardous components, and the hardest-to-remove impurities. For the most effective immobilization and even distribution of the analytes onto a nanostructured metallic surface, an additional polymer layer of chitosan was found to be needed. The presence of thin films of chitosan resulted in higher reproducibility of SERS spectra as compared to bare nanostructured silver substrates. Additionally, the developed nanocomposite SERS sensors provided the rapid determination of dibenzothiophene and its derivatives in isooctane with the threshold of detection better than 0.1 μM. This approach was successfully applied in the analysis of real fuel samples and the results agreed well with independently measured FTIR and GC-MS data.