Microfluidic devices are powerful bioapplication tools for cellular experiments in particular, as they can regulate physical and chemical parameters such as the flow rate, shear stress, oxygen, and molecular concentrations in a culture medium to mimic physiological and pathological microenvironments in vitro. However, as cell cultures take place in enclosed spaces, culture samples have to be removed repeatedly to monitor cell-derived metabolites and proteins in order to maintain the cellular microenvironment. We report a simple method for obtaining surface enhanced Raman scattering (SERS) spectra through self-assembly of a nanoparticle monolayer on polydimethylsiloxane (PDMS), which is commonly used in highly biocompatible microfluidic devices. Silica nanoparticles were stabilized as a hexagonal close packed structure on an O₂ plasma-processed PDMS membrane, and was coated with silver using vapor deposition to create an SERS plate. When this SERS plate was installed in a microfluidic device, the nanoparticles did not peel off even after long-term fluid immersion. The SERS spectra exhibited stable SERS generation and an enhancement factor of more than 1.5 × 10⁶ of the Raman signals from rhodamine 6G compared to the signals without nanoparticles. The SERS spectra of lactate and ATP were obtained, and Raman shifts due to the different masses of ¹²C- and ¹³C-lactate were observed, suggesting that the proposed method can be applied to determine the cellular metabolic flux in microfluidic devices. We also obtained cell membrane-derived SERS spectra by culturing murine mammary carcinoma 4T1 cells directly on the nanoparticle membrane. PDMS has high biocompatibility and is often used for fabricating microfluidic devices. Through tight binding of the nanoparticles to the O₂ plasma-treated PDMS, the chemical reaction products or the metabolites from cells can be measured for a long duration, while maintaining the microenvironment. We anticipate that this technology can be utilized as a useful tool for analyzing cellular metabolic functions and imaging cellular distributions without staining in various pathological models created in microfluidic devices.