The stability of surface-enhanced Raman spectroscopy (SERS) substrates in different organic solvents and different buffer solutions was investigated. SERS substrates were fabricated by a microwave-assisted synthesis approach and the morphological as well as chemical changes of the SERS substrates were studied. It was demonstrated that the SERS substrates treated with methanol, ethanol, or N,N-dimethylformamide (DMF) were comparable and showed overall good stability and did not show severe morphological changes or a strong decrease in their Raman activity. Toluene treatment resulted in a strong decrease in the Raman activity whereas dimethyl sulfoxide (DMSO) treatment completely preserved or even slightly improved the Raman enhancement capabilities. SERS substrates immersed into phosphate-buffered saline (PBS) solutions were observed to be rather instable in low and neutral pH buffer solutions. Other buffer systems showed less severe influences on the SERS activity of the substrates and a carbonate buffer at pH 10 was found to even improve SERS performance. This study represents a guideline on the stability of microwave-fabricated SERS substrates or other SERS substrates consisting of non-stabilized silver nanoparticles for the application of different organic solvents and buffer solutions.