Flexible surface enhanced Raman scattering (SERS) substrates have advantage over the conventional rigid substrates as they can conform to the underlying object for the efficient extraction of target molecules from complex surfaces. Here, we demonstrate a simple and facile method for fabricating large area SERS-active, flexible and robust substrate for conformal and rapid extraction and detection of trace molecules. The novel SERS substrate was fabricated by embedding Ag nanorods into the polydimethylsiloxane (PDMS) polymer. The AgNRs embedded SERS substrates exhibited a high sensitivity and excellent reproducibility for analytes employed, demonstrating a direct application in trace detection for on-field applications. The in situ SERS measurements on these flexible substrates under mechanical tensile strain conditions were performed. Our results show that flexible SERS substrates can withstand a tensile strain (ε) value as high as 30% without losing SERS performance. The functionality of AgNRs embedded PDMS SERS substrate was demonstrated by directly extracting trace amount (∼10−9 g/cm2) of thiram pesticide directly from fruit peels via simple “paste and peel off” method.