Functionalized plasmonic nanostructure platforms are widely used for developing optical biosensors and SERS assays. In this work, we present a low-cost and scalable surface-enhanced Raman scattering (SERS) system based on an innovative optical transducer comprising gold nanoparticles (AuNPs) embedded in nano-fibrillated bacterial cellulose (BC). The AuNPs@BC composite leverages the unique nanofibrillar architecture of bacterial cellulose, which provides a high surface area, flexibility, and uniform nanoparticle distribution, enabling the formation of numerous electromagnetic “hot spots”. This structure excites localized surface plasmon resonance (LSPR), as demonstrated by a bulk sensitivity of 72 nm/RIU, and supports enhanced Raman signal amplification. The eco-friendly and disposable AuNPs@BC platform was tested for agrifood applications, focusing on the detection of thiram pesticide. The system achieved a detection limit of 0.24 ppm (1 µM), meeting the sensitivity requirements for regulatory compliance in food safety. A strong linear correlation (R2 ≈ 0.99) was observed between the SERS peak intensity at 1370 cm−1 and thiram concentrations, underscoring its potential for quantitative analysis. The combination of high sensitivity, reproducibility, and environmental sustainability makes the AuNPs@BC platform a promising solution for developing cost-effective, flexible, and portable sensors for pesticide monitoring and other biosensing applications.